Citrus Sinensis ID: 013837

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-----
Protein Sequence
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKSMKKY
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccEEEEEEccHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccccccccccEccccccccccccccccccccccccccccccccccccccccccccccHccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccHHcccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHHHHHHcccccccccEEEEEEccccccEEEEEEccHHHHHHHHHcccEEEccEEEEEEcccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHHHHcccEEccEEcEEEEccccccccccccccHcccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgfdmappaaamlpgaavpgqlpgvpsavpemaqnmlpfgatqlgafplmpvQVMTQQATRHARRvyvgglpplanEQAIATFFSQVMTaiggnsagpgdAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAvrvrrptdynptlaaalgpgqpspnlnLAAVGLasgaiggaegpdrvfvgglpyyfTETQIKELLESFgtlhgfdlvkdrdtgnskgygfcvyqdpavtDIACAALNglkmgdktLTVRRatassgqsktEQESILAQAQQHIAIQKMALQTsgmntlgggmslFGETLAKVLCLTEMMKSMKKY
Flexible Loop (DISEMBL)
msgrdirydavgegsrhksswvsgrsrtgergrdrhhrdfksggddrrrdknykydregirdhdrtdrhrdynrdkerrhrhrsrshssdrfrnrskslspsrspskskrrsgFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATassgqskteQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKSMKKY
Low Complexity Region (SEG)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGddrrrdknykydrEGIrdhdrtdrhrdynrdKErrhrhrsrshssdrfrnrskslspsrspskskrrsGFDmappaaamlpgaavpgQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESilaqaqqhiaiqKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKSMKKY
Disordered region (IsUnstruct)
**************************************************************************************************************************************************MLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM*************GIIFEGVAVRVRRPTDYNPTLAAAL********LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL*************************HIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTE********
Disordered Region (DISOPRED)
*******************************************************************************************************************************************************************************RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRP***************************************RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV*****************************************************VLCLTEMMKSM***
Disordered Region (DISEMBL)
***********************************************RRDKNYKYDREGIRDHDRTDRHRDYN*****************************************DMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV*******************QAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKSMKKY
Disordered Region (DISPRO)
****************************************************************************************************************GFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPF*******FPLMPV*******TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTD********************************AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA***********************K****T**************ETLAKVLCLTEMMKSMKKY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKSMKKY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	435	2.2.26 [Sep-21-2011]
Q9ZR39	555	Splicing factor U2af larg	N/A	no	0.701	0.549	0.711	1e-131
Q9ZR40	573	Splicing factor U2af larg	N/A	no	0.705	0.535	0.700	1e-130
Q8L716	589	Splicing factor U2af larg	yes	no	0.703	0.519	0.689	1e-127
O23212	573	Splicing factor U2af larg	no	no	0.708	0.537	0.68	1e-121
Q2QKB4	543	Splicing factor U2af larg	N/A	no	0.721	0.578	0.672	1e-119
Q2QZL4	548	Splicing factor U2af larg	yes	no	0.698	0.554	0.678	1e-118
Q2QKB3	591	Splicing factor U2af larg	N/A	no	0.875	0.644	0.562	1e-113
Q2R0Q1	574	Splicing factor U2af larg	no	no	0.657	0.498	0.664	1e-112
P26369	475	Splicing factor U2AF 65 k	yes	no	0.687	0.629	0.382	5e-49
P26368	475	Splicing factor U2AF 65 k	yes	no	0.687	0.629	0.382	5e-49

>sp|Q9ZR39|U2A2A_NICPL Splicing factor U2af large subunit A OS=Nicotiana plumbaginifolia GN=U2AF65A PE=2 SV=1

 Score =  469 bits (1207), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 227/319 (71%), Positives = 256/319 (80%), Gaps = 14/319 (4%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP  A+LPGA    GQ+PG   A+P +  NM P  ++Q GA P+MPVQ MTQQA
Sbjct: 157 SGFDMAPPTTALLPGATDAAGQVPGTNPAIPGLFSNMFPLASSQFGALPMMPVQAMTQQA 216

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 217 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 276

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVG   G+ GG
Sbjct: 277 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGSTPGSSGG 336

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 337 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 396

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 411 GMSLFGETLAKVLCLTEMM 429
                     KVLCLTE++
Sbjct: 454 ----------KVLCLTEVV 462

Necessary for the splicing of pre-mRNA. Binds to the U -enriched regions of plant introns.
Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q9ZR40|U2A2B_NICPL Splicing factor U2af large subunit B OS=Nicotiana plumbaginifolia GN=U2AF65B PE=2 SV=1

 Score =  463 bits (1192), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 225/321 (70%), Positives = 258/321 (80%), Gaps = 14/321 (4%)

Query: 112 SGFDMAPPAAAMLPG-AAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +AMLPG  A  GQ+PG    +P M  NM P  + Q GA P+MP+Q MTQQA
Sbjct: 175 SGFDMAPPTSAMLPGITAAAGQVPGTNPPIPGMFPNMFPLASGQFGALPVMPIQAMTQQA 234

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLP  ANEQ++ATFFS VM+AIGGN+AGPGDAVVNVYIN+EKKFAFVEMR
Sbjct: 235 TRHARRVYVGGLPAHANEQSVATFFSHVMSAIGGNTAGPGDAVVNVYINYEKKFAFVEMR 294

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDGIIFEG   +VRRP+DYNP+LAA LGP QP+PNLNLAAVGL+ G+ GG
Sbjct: 295 SVEEASNAMALDGIIFEGAPCKVRRPSDYNPSLAATLGPSQPNPNLNLAAVGLSPGSAGG 354

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 355 LEGPDRIFVGGLPYYFTEAQIRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 414

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+Q++ LQ + + T   
Sbjct: 415 IACAALNGIKMGDKTLTVRRANQGTTQPKPEQESVLLHAQQQIALQRLMLQPATLAT--- 471

Query: 411 GMSLFGETLAKVLCLTEMMKS 431
                     KVL LTE++ +
Sbjct: 472 ----------KVLSLTEVISA 482

Necessary for the splicing of pre-mRNA. Binds to the U -enriched regions of plant introns.

Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q8L716|U2A2B_ARATH Splicing factor U2af large subunit B OS=Arabidopsis thaliana GN=U2AF65B PE=2 SV=2

 Score =  456 bits (1172), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 222/322 (68%), Positives = 255/322 (79%), Gaps = 16/322 (4%)

Query: 113 GFDMAPPAAAMLPGAAVPGQLPGVPSA--VPEMAQNMLPF-GATQLGAFPLMPVQVMTQQ 169
           GFDMAPP        A  GQ+P VP+   +P M  NM P     QLGA P++PVQ MTQQ
Sbjct: 190 GFDMAPPDMLAATAVAAAGQVPSVPTTATIPGMFSNMFPMVPGQQLGALPVLPVQAMTQQ 249

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           ATRHARRVYVGGLPP ANEQ+++TFFSQVM+AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct: 250 ATRHARRVYVGGLPPTANEQSVSTFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEM 309

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           R+VEEASNAMALDGII EGV V+VRRPTDYNP+LAA LGP QP+PNLNL AVGL+SG+ G
Sbjct: 310 RSVEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNLNLGAVGLSSGSTG 369

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EGPDR+FVGGLPYYFTE QI+ELLESFG L GF+LVKDR+TGNSKGY FCVYQDP+VT
Sbjct: 370 GLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSVT 429

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 409
           DIACAALNG+KMGDKTLTVRRA   + Q K EQE +L  AQQ IA+Q++  Q  G     
Sbjct: 430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGG----- 484

Query: 410 GGMSLFGETLAKVLCLTEMMKS 431
                   T  K++CLT+++ +
Sbjct: 485 --------TPTKIVCLTQVVTA 498

Necessary for the splicing of pre-mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|O23212|U2A2A_ARATH Splicing factor U2af large subunit A OS=Arabidopsis thaliana GN=U2AF65A PE=2 SV=2

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 221/325 (68%), Positives = 254/325 (78%), Gaps = 17/325 (5%)

Query: 109 KRRSGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPE--MAQNMLPFGATQ-LGAFPLMPVQ 164
           +R SGFDMAPPA+AML   A V GQ+P  P  +P   M  NM P    Q  G   +MP+Q
Sbjct: 169 QRVSGFDMAPPASAMLAAGAAVTGQVPPAPPTLPGAGMFPNMFPLPTGQSFGGLSMMPIQ 228

Query: 165 VMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF 224
            MTQQATRHARRVYVGGL P ANEQ++ATFFSQVM A+GGN+AGPGDAVVNVYINHEKKF
Sbjct: 229 AMTQQATRHARRVYVGGLSPTANEQSVATFFSQVMAAVGGNTAGPGDAVVNVYINHEKKF 288

Query: 225 AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           AFVEMR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP+LAA LGP QPSP+LNLAAVGL 
Sbjct: 289 AFVEMRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNPSLAATLGPSQPSPHLNLAAVGLT 348

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
            GA GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQ
Sbjct: 349 PGASGGLEGPDRIFVGGLPYYFTESQVRELLESFGGLKGFDLVKDRETGNSKGYAFCVYQ 408

Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSG 404
           D +VTDIACAALNG+KMGDKTLTVRRA   +   K EQE++L  AQQ IA Q++ LQ   
Sbjct: 409 DLSVTDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGA 468

Query: 405 MNTLGGGMSLFGETLAKVLCLTEMM 429
           + T              V+CLT+++
Sbjct: 469 VATT-------------VVCLTQVV 480

Necessary for the splicing of pre-mRNA.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QKB4|U2A2B_WHEAT Splicing factor U2af large subunit B OS=Triticum aestivum GN=U2AF65B PE=2 SV=1

 Score =  430 bits (1105), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 224/333 (67%), Positives = 259/333 (77%), Gaps = 19/333 (5%)

Query: 102 SRSPSKSKRRSGFDMAPPAAAMLP---GAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAF 158
           SRS SKSKR SGFD+ P A ++LP       P QLPG  S++P M  NMLPF   Q+   
Sbjct: 134 SRSHSKSKRVSGFDLGPTAQSVLPQFPTIPTPSQLPG--SSIPGMFPNMLPFADGQINPL 191

Query: 159 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            + P Q MTQQATRHARRVYVGGLPP ANEQ++A +F+QVM AIGGN+AGPGDAV+NVYI
Sbjct: 192 VMQP-QAMTQQATRHARRVYVGGLPPSANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYI 250

Query: 219 NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNL 278
           NH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+LAAALGP QPS NLNL
Sbjct: 251 NHDKKFAFVEMRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSSNLNL 310

Query: 279 AAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
           AAVGL  G+ GG EGPDR+FVGGLPYYFTE Q++ELLESFG L GFDLVKDR+TGNSKGY
Sbjct: 311 AAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSKGY 370

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKM 398
            FCVYQD  VTDIACAALNG+KMGDKTLTVRRA   S Q + EQE+IL QAQQ + +QK+
Sbjct: 371 AFCVYQDLNVTDIACAALNGIKMGDKTLTVRRANQGSAQPRPEQENILLQAQQQVQLQKL 430

Query: 399 ALQTSGMNTLGGGMSLFGETLAKVLCLTEMMKS 431
             Q   + T             KV+CLT+++ +
Sbjct: 431 VYQVGALPT-------------KVVCLTQVVTA 450

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|Q2QZL4|U2A2B_ORYSJ Splicing factor U2af large subunit B OS=Oryza sativa subsp. japonica GN=U2AF65B PE=2 SV=2

 Score =  425 bits (1093), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 219/323 (67%), Positives = 252/323 (78%), Gaps = 19/323 (5%)

Query: 112 SGFDMAPPAAAMLP---GAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQ 168
           SGFDMAPPA A++P       P Q PG  +A+P M  NMLP G  Q     + P Q MTQ
Sbjct: 151 SGFDMAPPAQAVVPQFPAIPTPSQFPG--TAIPGMFPNMLPMGVGQFNPLVIQP-QAMTQ 207

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           QATRHARRVYVGGLPP ANEQ++A +F+QVM AIGGN+AGPGDAV+NVYINH+KKFAFVE
Sbjct: 208 QATRHARRVYVGGLPPTANEQSVAIYFNQVMAAIGGNTAGPGDAVLNVYINHDKKFAFVE 267

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
           MR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+LAAALGP QPSPNLNLAAVGL  G+ 
Sbjct: 268 MRSVEEASNAMALDGILFEGAPVKVRRPTDYNPSLAAALGPSQPSPNLNLAAVGLTPGSA 327

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GG EGPDR+FVGGLPYYFTE Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQD  V
Sbjct: 328 GGLEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDLNV 387

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTL 408
           TDIACAALNG+KMGDKTLTVRRA   + Q + EQESIL QAQQ + +QK+  Q   + T 
Sbjct: 388 TDIACAALNGIKMGDKTLTVRRANQGAAQPRPEQESILLQAQQQVQLQKLVYQVGALPT- 446

Query: 409 GGGMSLFGETLAKVLCLTEMMKS 431
                       KV+CLT+++ +
Sbjct: 447 ------------KVVCLTQVVSA 457

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q2QKB3|U2A2A_WHEAT Splicing factor U2af large subunit A OS=Triticum aestivum GN=U2AF65A PE=2 SV=1

 Score =  410 bits (1053), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 229/407 (56%), Positives = 275/407 (67%), Gaps = 26/407 (6%)

Query: 29  GERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHS 88
           G R R+RHHRD + G  DR R   +  D     +        D    +    R   R   
Sbjct: 131 GSRDRERHHRDHREGSRDRER---HHRDHRERSERREHRDRSDDRDYRRSCDRDAERRDR 187

Query: 89  SDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAA-AMLPGAAVPGQLPGVPSAVPEMAQNM 147
                 R +S SP RS S+SKR SGFD  P  A  +L   A P QLP +P+A P M  NM
Sbjct: 188 DRDGHRRHRSRSPLRSESQSKRMSGFDQRPSEAIPILAPDATPSQLPELPAANPGMFPNM 247

Query: 148 LP--FGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGN 205
           LP       LG  PL     MTQQATRHARRVYVGGLPP+ANEQ +A FF+QVM AIGGN
Sbjct: 248 LPNLVNVPALGQ-PL----AMTQQATRHARRVYVGGLPPIANEQTVAVFFNQVMAAIGGN 302

Query: 206 SAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAA 265
           +   G AVVNVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V+VRRPTDYNP+ AA
Sbjct: 303 TFALGHAVVNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPVKVRRPTDYNPSQAA 362

Query: 266 ALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD 325
           ALGP QP+PNLNLAAVGL  GA GG EGPDR+FVGGLPYYFTE Q++ELLE+FG L GFD
Sbjct: 363 ALGPSQPNPNLNLAAVGLTPGAGGGLEGPDRIFVGGLPYYFTEAQVRELLETFGPLRGFD 422

Query: 326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESI 385
           +VKD++TGNSKGY FC+Y+D  VTDIACAALNG+++GD+TLTVRRA     + + EQE+I
Sbjct: 423 IVKDKETGNSKGYAFCLYKDGTVTDIACAALNGIQLGDRTLTVRRAN-QGAEPRPEQENI 481

Query: 386 LAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETL-AKVLCLTEMMKS 431
           L QAQQ   ++++  +              G TL  KV+CLT+++ +
Sbjct: 482 LLQAQQEAQMKRLVYEV-------------GRTLTTKVVCLTQVVSA 515

Necessary for the splicing of pre-mRNA.

Triticum aestivum (taxid: 4565)

>sp|Q2R0Q1|U2A2A_ORYSJ Splicing factor U2af large subunit A OS=Oryza sativa subsp. japonica GN=U2AF65A PE=2 SV=2

 Score =  405 bits (1042), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 198/298 (66%), Positives = 228/298 (76%), Gaps = 12/298 (4%)

Query: 132 QLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           Q+P V  A+  M  NM     T      + P Q MTQQATRHARRVYVGGLPP ANE  +
Sbjct: 196 QVPVVAPAISGMLPNMFNLTQTPFTPLVIQP-QAMTQQATRHARRVYVGGLPPTANEHTV 254

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV 251
           A +F+QVM A+GGN+AGPGDAV+NVYINH+KKFAFVEMR+VEEASNAMALDGI+FEG  V
Sbjct: 255 AVYFNQVMAAVGGNTAGPGDAVLNVYINHDKKFAFVEMRSVEEASNAMALDGIMFEGAPV 314

Query: 252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQI 311
           +VRRPTDYNP+LAAALGP QP+PNLNLAAVGL  G+ GG EGPDR+FVGGLPYYFTE Q+
Sbjct: 315 KVRRPTDYNPSLAAALGPSQPNPNLNLAAVGLTPGSAGGLEGPDRIFVGGLPYYFTEAQV 374

Query: 312 KELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +ELLESFG L GFDLVKDR+TGNSKGY FCVYQD  VTDIACAALNG+KMGDKTLTVRRA
Sbjct: 375 RELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDLNVTDIACAALNGIKMGDKTLTVRRA 434

Query: 372 TASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMM 429
              + Q + EQES+L   QQ   +QK+  Q  G           G    KV+CLT+++
Sbjct: 435 NQGASQPRPEQESMLLHVQQQAQMQKLMFQVGG-----------GALPTKVVCLTQVV 481

Necessary for the splicing of pre-mRNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|P26369|U2AF2_MOUSE Splicing factor U2AF 65 kDa subunit OS=Mus musculus GN=U2af2 PE=1 SV=3

 Score =  195 bits (496), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 128/335 (38%), Positives = 179/335 (53%), Gaps = 36/335 (10%)

Query: 103 RSP---SKSKRRSGFDMAPPAAAMLP-----GAAVPGQLPGVPSAVPEMAQNMLPFGATQ 154
           RSP    K K R  +D+ PP    +           GQ+P   + +P M  + L    T 
Sbjct: 78  RSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPAT-ALLPTMTPDGLAVTPT- 135

Query: 155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV 214
                  PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+
Sbjct: 136 -------PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVL 187

Query: 215 NVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSP 274
            V IN +K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S 
Sbjct: 188 AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SE 240

Query: 275 NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN 334
           N ++   G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG 
Sbjct: 241 NPSVYVPGVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 298

Query: 335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA 394
           SKGY FC Y D  VTD A A LNG+++GDK L V+RA+  +      + + L      I 
Sbjct: 299 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTIN 352

Query: 395 IQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMM 429
              + LQ  G+ +    M   G    +VLCL  M+
Sbjct: 353 QTPVTLQVPGLMSSQVQM---GGHPTEVLCLMNMV 384

Necessary for the splicing of pre-mRNA. Induces cardiac troponin-T (TNNT2) pre-mRNA exon inclusion in muscle. Regulates the TNNT2 exon 5 inclusion through competition with MBNL1. Binds preferentially to a single-stranded structure within the polypyrimidine tract of TNNT2 intron 4 during spliceosome assembly. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Represses the splicing of MAPT/Tau exon 10.

Mus musculus (taxid: 10090)

>sp|P26368|U2AF2_HUMAN Splicing factor U2AF 65 kDa subunit OS=Homo sapiens GN=U2AF2 PE=1 SV=4

 Score =  195 bits (496), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 128/335 (38%), Positives = 179/335 (53%), Gaps = 36/335 (10%)

Query: 103 RSP---SKSKRRSGFDMAPPAAAMLP-----GAAVPGQLPGVPSAVPEMAQNMLPFGATQ 154
           RSP    K K R  +D+ PP    +           GQ+P   + +P M  + L    T 
Sbjct: 78  RSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPAT-ALLPTMTPDGLAVTPT- 135

Query: 155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV 214
                  PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+
Sbjct: 136 -------PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVL 187

Query: 215 NVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSP 274
            V IN +K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S 
Sbjct: 188 AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SE 240

Query: 275 NLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN 334
           N ++   G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG 
Sbjct: 241 NPSVYVPGVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 298

Query: 335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA 394
           SKGY FC Y D  VTD A A LNG+++GDK L V+RA+  +      + + L      I 
Sbjct: 299 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTIN 352

Query: 395 IQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMM 429
              + LQ  G+ +    M   G    +VLCL  M+
Sbjct: 353 QTPVTLQVPGLMSSQVQM---GGHPTEVLCLMNMV 384

Necessary for the splicing of pre-mRNA. Induces cardiac troponin-T (TNNT2) pre-mRNA exon inclusion in muscle. Regulates the TNNT2 exon 5 inclusion through competition with MBNL1. Binds preferentially to a single-stranded structure within the polypyrimidine tract of TNNT2 intron 4 during spliceosome assembly. Required for the export of mRNA out of the nucleus, even if the mRNA is encoded by an intron-less gene. Represses the splicing of MAPT/Tau exon 10.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	435
359497050	410	PREDICTED: splicing factor U2af large su	0.689	0.731	0.873	1e-152
296088196	412	unnamed protein product [Vitis vinifera]	0.685	0.723	0.823	1e-141
388520789	527	unknown [Lotus japonicus]	0.912	0.753	0.648	1e-137
156070760	553	unknown [Solanum melongena]	0.781	0.614	0.676	1e-131
188998293	554	U2 snRNP auxiliary factor large subunit	0.781	0.613	0.676	1e-131
156070776	551	unknown [Capsicum frutescens]	0.701	0.553	0.717	1e-131
75338883	555	RecName: Full=Splicing factor U2af large	0.701	0.549	0.711	1e-129
156070797	558	unknown [Solanum bulbocastanum]	0.701	0.546	0.712	1e-129
156070781	557	unknown [Petunia integrifolia subsp. inf	0.701	0.547	0.708	1e-129
449496757	587	PREDICTED: splicing factor U2af large su	0.698	0.517	0.714	1e-129

>gi|359497050|ref|XP_002267854.2| PREDICTED: splicing factor U2af large subunit B-like, partial [Vitis vinifera]

 Score =  544 bits (1401), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 262/300 (87%), Positives = 277/300 (92%)

Query: 112 SGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQAT 171
           SGFDMAPP AA+LPGAAVPG+LPGVP  VP M QNM PFGATQLGA PLMPVQ MTQQAT
Sbjct: 44  SGFDMAPPVAALLPGAAVPGELPGVPQMVPGMIQNMFPFGATQLGALPLMPVQAMTQQAT 103

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           RHARRVYVGGLPPLANEQ IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR+
Sbjct: 104 RHARRVYVGGLPPLANEQTIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRS 163

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGA 291
           VEEASNAMALDGI+FEGV+VRVRRPTDYNP+LAAALGP QPSP+LNLAAVGL  G IGGA
Sbjct: 164 VEEASNAMALDGIMFEGVSVRVRRPTDYNPSLAAALGPSQPSPHLNLAAVGLMPGVIGGA 223

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           EGPDR+FVGGLPYYFTE QI+ELLESFG L GFDLVKDRDTGNSKGYGFCVYQDPAVTDI
Sbjct: 224 EGPDRIFVGGLPYYFTEEQIRELLESFGPLRGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 283

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 411
           ACAALNGLKMGDKTLTVRRAT  SGQ+K+EQ++ILAQAQQHIAIQK+ALQ  G+N  G G
Sbjct: 284 ACAALNGLKMGDKTLTVRRATVGSGQAKSEQDNILAQAQQHIAIQKIALQAGGLNLPGAG 343

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296088196|emb|CBI35712.3| unnamed protein product [Vitis vinifera]

 Score =  506 bits (1303), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 248/301 (82%), Positives = 264/301 (87%), Gaps = 3/301 (0%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
           G+LPGVP  VP M QNM PFGATQLGA PLMPVQ MTQQATRHARRVYVGGLPPLANEQ 
Sbjct: 105 GELPGVPQMVPGMIQNMFPFGATQLGALPLMPVQAMTQQATRHARRVYVGGLPPLANEQT 164

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA 250
           IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDGI+FE   
Sbjct: 165 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGIMFEACL 224

Query: 251 VRV-RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTET 309
             +   PTDYNP+LAAALGP QPSP+LNLAAVGL  G IGGAEGPDR+FVGGLPYYFTE 
Sbjct: 225 TLIFSLPTDYNPSLAAALGPSQPSPHLNLAAVGLMPGVIGGAEGPDRIFVGGLPYYFTEE 284

Query: 310 QIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR 369
           QI+ELLESFG L GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR
Sbjct: 285 QIRELLESFGPLRGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR 344

Query: 370 RATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSL--FGETLAKVLCLTE 427
           RAT  SGQ+K+EQ++ILAQAQQHIAIQK+ALQ  G+N  G GM+     ET  KVLCLTE
Sbjct: 345 RATVGSGQAKSEQDNILAQAQQHIAIQKIALQAGGLNLPGAGMAFTAIAETPTKVLCLTE 404

Query: 428 M 428
           +
Sbjct: 405 V 405

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388520789|gb|AFK48456.1| unknown [Lotus japonicus]

 Score =  496 bits (1276), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 268/413 (64%), Positives = 315/413 (76%), Gaps = 16/413 (3%)

Query: 25  RSRTGER--GRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           R + GER    DRHHRD+K GG + R D+   Y+R   RD+DR   H D  +D ERRH++
Sbjct: 34  RKQDGERRDFHDRHHRDYKDGGFNGR-DRYNSYNRHRSRDYDR---HNDRVKDGERRHKY 89

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPE 142
            + S    R R  S+S S S S S+SKR SGFDMAPP+A     +AV GQ  G+      
Sbjct: 90  EAHS---KRSRGESRSPSRSPSRSESKRVSGFDMAPPSADGT--SAVSGQTLGINHLNQG 144

Query: 143 MAQNMLPFGATQ--LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMT 200
            AQN   FG +Q  +GA  LM VQ MTQQATRHARRVY+GGLPPL NEQ+IATFFS VMT
Sbjct: 145 TAQNFSLFGISQPQIGALSLMQVQPMTQQATRHARRVYIGGLPPLTNEQSIATFFSHVMT 204

Query: 201 AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYN 260
           AIGGNSAG GD+VVNVYINHEKKFAF+EMRTVEEASNAM+LDGI+FEGV+VRVRRPTDYN
Sbjct: 205 AIGGNSAGAGDSVVNVYINHEKKFAFLEMRTVEEASNAMSLDGIVFEGVSVRVRRPTDYN 264

Query: 261 PTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT 320
           PTLAAALGP QPSP LNL+AVGL+ G IGG +G DR+FVGGLPYYF E QI+ELL++FG 
Sbjct: 265 PTLAAALGPCQPSPYLNLSAVGLSGGTIGGTDGLDRIFVGGLPYYFAEEQIRELLQAFGP 324

Query: 321 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 380
           L  FDLV+D++TGNSKGYGFC+YQDPAVTD+ACA+LNGLK+GDKTLTVRRAT  SG SKT
Sbjct: 325 LRSFDLVRDKETGNSKGYGFCIYQDPAVTDMACASLNGLKVGDKTLTVRRATV-SGHSKT 383

Query: 381 EQESILAQAQQHIAIQKMALQTSGMNTLGGGM--SLFGETLAKVLCLTEMMKS 431
           EQE I AQAQQ+I +QK+AL+  G+N  G     +   E+  KVLCLTE + +
Sbjct: 384 EQEHIFAQAQQNITMQKVALEVVGLNIPGVERVPTTIDESATKVLCLTEAITT 436

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070760|gb|ABU45175.1| unknown [Solanum melongena]

 Score =  474 bits (1220), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 247/365 (67%), Positives = 284/365 (77%), Gaps = 25/365 (6%)

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPG 126
           DR R+ ++D+E RHRH+  S +  R          SRSPSKSKR SGFDMAPP +A+L G
Sbjct: 117 DRRRNNDKDREDRHRHKPSSRARSR----------SRSPSKSKRISGFDMAPPTSALLSG 166

Query: 127 AA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPP 184
           A  V GQ+PG+ + ++P M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP
Sbjct: 167 ATDVAGQVPGITNPSIPGMFSNMFPVAAGQFGALPVMPVQAMTQQATRHARRVYVGGLPP 226

Query: 185 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI 244
            ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+
Sbjct: 227 TANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGV 286

Query: 245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPY 304
           IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPY
Sbjct: 287 IFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPY 346

Query: 305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK 364
           YFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDK
Sbjct: 347 YFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDK 406

Query: 365 TLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 424
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 407 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 453

Query: 425 LTEMM 429
           LT+++
Sbjct: 454 LTQVV 458

Source: Solanum melongena

Species: Solanum melongena

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|188998293|gb|ACD67872.1| U2 snRNP auxiliary factor large subunit [Solanum melongena]

 Score =  474 bits (1220), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 247/365 (67%), Positives = 284/365 (77%), Gaps = 25/365 (6%)

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPG 126
           DR R+ ++D+E RHRH+  S +  R          SRSPSKSKR SGFDMAPP +A+L G
Sbjct: 118 DRRRNNDKDREDRHRHKPSSRARSR----------SRSPSKSKRISGFDMAPPTSALLSG 167

Query: 127 AA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPP 184
           A  V GQ+PG+ + ++P M  NM P  A Q GA P+MPVQ MTQQATRHARRVYVGGLPP
Sbjct: 168 ATDVAGQVPGITNPSIPGMFSNMFPVAAGQFGALPVMPVQAMTQQATRHARRVYVGGLPP 227

Query: 185 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI 244
            ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR+VEEASNAMALDG+
Sbjct: 228 TANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMRSVEEASNAMALDGV 287

Query: 245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPY 304
           IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG EGPDR+FVGGLPY
Sbjct: 288 IFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGGLEGPDRIFVGGLPY 347

Query: 305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK 364
           YFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTDIACAALNG+KMGDK
Sbjct: 348 YFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTDIACAALNGIKMGDK 407

Query: 365 TLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLC 424
           TLTVRRA     Q   EQES+L  AQQ IA+Q+  LQ   + T             K+LC
Sbjct: 408 TLTVRRANQGITQPNPEQESVLLHAQQQIALQRFMLQPGALAT-------------KILC 454

Query: 425 LTEMM 429
           LT+++
Sbjct: 455 LTQVV 459

Source: Solanum melongena

Species: Solanum melongena

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070776|gb|ABU45190.1| unknown [Capsicum frutescens]

 Score =  474 bits (1219), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 229/319 (71%), Positives = 258/319 (80%), Gaps = 14/319 (4%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +A+LPGA  V GQ+PG   ++P M  NM P  A Q GA P+MPVQ MTQQA
Sbjct: 153 SGFDMAPPTSALLPGATDVTGQVPGANPSIPGMFSNMFPLAAGQFGALPIMPVQAMTQQA 212

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 213 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 272

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG
Sbjct: 273 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGG 332

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 333 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 392

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 393 IACAALNGIKMGDKTLTVRRANQGTNQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 449

Query: 411 GMSLFGETLAKVLCLTEMM 429
                     KVLCLT+++
Sbjct: 450 ----------KVLCLTQVV 458

Source: Capsicum frutescens

Species: Capsicum frutescens

Genus: Capsicum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75338883|sp|Q9ZR39.1|U2A2A_NICPL RecName: Full=Splicing factor U2af large subunit A; AltName: Full=NpU2AF65a; AltName: Full=U2 auxiliary factor 65 kDa subunit A; AltName: Full=U2 small nuclear ribonucleoprotein auxiliary factor large subunit A; Short=U2 snRNP auxiliary factor large subunit A gi|3850823|emb|CAA77136.1| U2 snRNP auxiliary factor, large subunit [Nicotiana plumbaginifolia]

 Score =  469 bits (1207), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 227/319 (71%), Positives = 256/319 (80%), Gaps = 14/319 (4%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP  A+LPGA    GQ+PG   A+P +  NM P  ++Q GA P+MPVQ MTQQA
Sbjct: 157 SGFDMAPPTTALLPGATDAAGQVPGTNPAIPGLFSNMFPLASSQFGALPMMPVQAMTQQA 216

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 217 TRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 276

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVG   G+ GG
Sbjct: 277 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGSTPGSSGG 336

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 337 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 396

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T   
Sbjct: 397 IACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT--- 453

Query: 411 GMSLFGETLAKVLCLTEMM 429
                     KVLCLTE++
Sbjct: 454 ----------KVLCLTEVV 462

Source: Nicotiana plumbaginifolia

Species: Nicotiana plumbaginifolia

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070797|gb|ABU45209.1| unknown [Solanum bulbocastanum]

 Score =  468 bits (1203), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 228/320 (71%), Positives = 258/320 (80%), Gaps = 15/320 (4%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPS-AVPEMAQNMLPFGATQLGAFPLMPVQVMTQQ 169
           SGFDMAPP +A+L GA  V GQ+PG  + ++P M  NM P  A Q GA P+MPVQ MTQQ
Sbjct: 159 SGFDMAPPTSALLSGATDVAGQVPGTTNPSIPGMFSNMFPLAAGQFGALPIMPVQAMTQQ 218

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           ATRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct: 219 ATRHARRVYVGGLPPTANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEM 278

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           R+VEEASNAMALDG++FEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ G
Sbjct: 279 RSVEEASNAMALDGVVFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSG 338

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VT
Sbjct: 339 GLEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVT 398

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLG 409
           DIACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+Q+  LQ   + T  
Sbjct: 399 DIACAALNGIKMGDKTLTVRRANQGTTQPNPEQESVLLHAQQQIALQRFMLQPGALAT-- 456

Query: 410 GGMSLFGETLAKVLCLTEMM 429
                      KVLCLTE++
Sbjct: 457 -----------KVLCLTEVV 465

Source: Solanum bulbocastanum

Species: Solanum bulbocastanum

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|156070781|gb|ABU45194.1| unknown [Petunia integrifolia subsp. inflata]

 Score =  467 bits (1202), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 226/319 (70%), Positives = 255/319 (79%), Gaps = 14/319 (4%)

Query: 112 SGFDMAPPAAAMLPGAA-VPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA 170
           SGFDMAPP +A+LPGA    GQ+PG   ++P M  NM P  + Q GA P+MP+Q MTQQA
Sbjct: 162 SGFDMAPPTSALLPGATDTAGQVPGASPSIPGMFSNMFPLTSGQFGALPVMPIQAMTQQA 221

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFS VM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 222 TRHARRVYVGGLPPSANEQSVATFFSHVMYAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 281

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDG+IFEG  V+VRRP+DYNP+LAA LGP QPSPNLNLAAVGL  G+ GG
Sbjct: 282 SVEEASNAMALDGVIFEGGPVKVRRPSDYNPSLAATLGPSQPSPNLNLAAVGLTPGSSGG 341

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE+QI+ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 342 LEGPDRIFVGGLPYYFTESQIRELLESFGQLRGFDLVKDRETGNSKGYAFCVYQDVSVTD 401

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q   EQES+L  AQQ IA+QK   Q   + T   
Sbjct: 402 IACAALNGIKMGDKTLTVRRANQGTPQPNPEQESVLLHAQQQIALQKFMFQPGALAT--- 458

Query: 411 GMSLFGETLAKVLCLTEMM 429
                     KVLCLT+ +
Sbjct: 459 ----------KVLCLTQAV 467

Source: Petunia integrifolia subsp. inflata

Species: Petunia integrifolia

Genus: Petunia

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449496757|ref|XP_004160219.1| PREDICTED: splicing factor U2af large subunit B-like [Cucumis sativus]

 Score =  467 bits (1201), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 228/319 (71%), Positives = 256/319 (80%), Gaps = 15/319 (4%)

Query: 113 GFDMAPPAAAMLPGA-AVPGQLPGVPSAVPEMAQNMLPFGATQ-LGAFPLMPVQVMTQQA 170
           GFDMAPP  A+L GA A  GQ+PG   A+P M   M P    Q  GA P+MPVQ MTQQA
Sbjct: 190 GFDMAPPTTAILSGATAAAGQIPGTTPAIPGMFPTMFPLATGQPFGALPVMPVQAMTQQA 249

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           TRHARRVYVGGLPP ANEQ++ATFFSQVM AIGGN+AGPGDAVVNVYINHEKKFAFVEMR
Sbjct: 250 TRHARRVYVGGLPPTANEQSVATFFSQVMAAIGGNTAGPGDAVVNVYINHEKKFAFVEMR 309

Query: 231 TVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
           +VEEASNAMALDGIIFEG  V+VRRP+DYNP+LAA LGP QP+PNLNLAAVGL  G+ GG
Sbjct: 310 SVEEASNAMALDGIIFEGAPVKVRRPSDYNPSLAATLGPSQPNPNLNLAAVGLTPGSAGG 369

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EGPDR+FVGGLPYYFTE Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +VTD
Sbjct: 370 LEGPDRIFVGGLPYYFTEAQVRELLESFGPLRGFDLVKDRETGNSKGYAFCVYQDLSVTD 429

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG 410
           IACAALNG+KMGDKTLTVRRA   + Q K EQES+L  AQQ IA+QK+ LQ   ++T   
Sbjct: 430 IACAALNGIKMGDKTLTVRRANQGANQPKPEQESVLLHAQQQIALQKLMLQPGAVST--- 486

Query: 411 GMSLFGETLAKVLCLTEMM 429
                     KVLCLT+++
Sbjct: 487 ----------KVLCLTQVV 495

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	435
TAIR|locus:2206001	589	AT1G60900 [Arabidopsis thalian	0.678	0.500	0.687	3e-110
TAIR|locus:2115280	573	ATU2AF65A [Arabidopsis thalian	0.678	0.514	0.658	4.6e-103
UNIPROTKB|Q24JZ8	475	U2AF2 "Uncharacterized protein	0.572	0.524	0.406	2e-47
MGI|MGI:98886	475	U2af2 "U2 small nuclear ribonu	0.572	0.524	0.406	2e-47
RGD|1597319	475	LOC690372 "similar to U2 (RNU2	0.572	0.524	0.406	2e-47
ZFIN|ZDB-GENE-050706-131	470	u2af2a "U2 small nuclear RNA a	0.577	0.534	0.406	2e-47
UNIPROTKB|P26368	475	U2AF2 "Splicing factor U2AF 65	0.572	0.524	0.406	2.6e-47
UNIPROTKB|E2R0G3	471	U2AF2 "Uncharacterized protein	0.468	0.433	0.467	4.2e-47
FB|FBgn0005411	416	U2af50 "U2 small nuclear ribop	0.535	0.560	0.407	1.8e-44
ZFIN|ZDB-GENE-040426-1881	475	u2af2b "U2 small nuclear RNA a	0.565	0.517	0.406	2.5e-42

TAIR|locus:2206001 AT1G60900 [Arabidopsis thaliana (taxid:3702)]

 Score = 1052 (375.4 bits), Expect = 3.0e-110, Sum P(2) = 3.0e-110
 Identities = 205/298 (68%), Positives = 230/298 (77%)

Query:   113 GFDXXXXXXXXXXXXXXXXQLPGVPSA--VPEMAQNMLPF-GATQLGAFPLMPVQVMTQQ 169
             GFD                Q+P VP+   +P M  NM P     QLGA P++PVQ MTQQ
Sbjct:   190 GFDMAPPDMLAATAVAAAGQVPSVPTTATIPGMFSNMFPMVPGQQLGALPVLPVQAMTQQ 249

Query:   170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
             ATRHARRVYVGGLPP ANEQ+++TFFSQVM+AIGGN+AGPGDAVVNVYINHEKKFAFVEM
Sbjct:   250 ATRHARRVYVGGLPPTANEQSVSTFFSQVMSAIGGNTAGPGDAVVNVYINHEKKFAFVEM 309

Query:   230 RTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
             R+VEEASNAMALDGII EGV V+VRRPTDYNP+LAA LGP QP+PNLNL AVGL+SG+ G
Sbjct:   310 RSVEEASNAMALDGIILEGVPVKVRRPTDYNPSLAATLGPSQPNPNLNLGAVGLSSGSTG 369

Query:   290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
             G EGPDR+FVGGLPYYFTE QI+ELLESFG L GF+LVKDR+TGNSKGY FCVYQDP+VT
Sbjct:   370 GLEGPDRIFVGGLPYYFTEVQIRELLESFGPLRGFNLVKDRETGNSKGYAFCVYQDPSVT 429

Query:   350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQTSGMNT 407
             DIACAALNG+KMGDKTLTVRRA   + Q K EQE             ++  Q  G  T
Sbjct:   430 DIACAALNGIKMGDKTLTVRRAIQGAIQPKPEQEEVLLYAQQQIALQRLMFQPGGTPT 487

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

TAIR|locus:2115280 ATU2AF65A [Arabidopsis thaliana (taxid:3702)]

 Score = 995 (355.3 bits), Expect = 4.6e-103, Sum P(2) = 4.6e-103
 Identities = 197/299 (65%), Positives = 223/299 (74%)

Query:   113 GFDXXX-XXXXXXXXXXXXXQLPGVPSAVPE--MAQNMLPFGATQ-LGAFPLMPVQVMTQ 168
             GFD                 Q+P  P  +P   M  NM P    Q  G   +MP+Q MTQ
Sbjct:   173 GFDMAPPASAMLAAGAAVTGQVPPAPPTLPGAGMFPNMFPLPTGQSFGGLSMMPIQAMTQ 232

Query:   169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
             QATRHARRVYVGGL P ANEQ++ATFFSQVM A+GGN+AGPGDAVVNVYINHEKKFAFVE
Sbjct:   233 QATRHARRVYVGGLSPTANEQSVATFFSQVMAAVGGNTAGPGDAVVNVYINHEKKFAFVE 292

Query:   229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
             MR+VEEASNAM+LDGIIFEG  V+VRRP+DYNP+LAA LGP QPSP+LNLAAVGL  GA 
Sbjct:   293 MRSVEEASNAMSLDGIIFEGAPVKVRRPSDYNPSLAATLGPSQPSPHLNLAAVGLTPGAS 352

Query:   289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
             GG EGPDR+FVGGLPYYFTE+Q++ELLESFG L GFDLVKDR+TGNSKGY FCVYQD +V
Sbjct:   353 GGLEGPDRIFVGGLPYYFTESQVRELLESFGGLKGFDLVKDRETGNSKGYAFCVYQDLSV 412

Query:   349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQTSGMNT 407
             TDIACAALNG+KMGDKTLTVRRA   +   K EQE+            ++ LQ   + T
Sbjct:   413 TDIACAALNGIKMGDKTLTVRRANQGTMLQKPEQENVLLHAQQQIAFQRVMLQPGAVAT 471

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0042742 "defense response to bacterium" evidence=IEP

GO:0000398 "mRNA splicing, via spliceosome" evidence=ISS

UNIPROTKB|Q24JZ8 U2AF2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 470 (170.5 bits), Expect = 2.0e-47, Sum P(2) = 2.0e-47
 Identities = 109/268 (40%), Positives = 155/268 (57%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPLSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+  +   + + G    +VLCL  M+
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMV 384

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

MGI|MGI:98886 U2af2 "U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2" [Mus musculus (taxid:10090)]

 Score = 470 (170.5 bits), Expect = 2.0e-47, Sum P(2) = 2.0e-47
 Identities = 109/268 (40%), Positives = 155/268 (57%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+  +   + + G    +VLCL  M+
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMV 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IDA

GO:0016607 "nuclear speck" evidence=TAS

GO:0019899 "enzyme binding" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=ISO

GO:0070742 "C2H2 zinc finger domain binding" evidence=IPI

RGD|1597319 LOC690372 "similar to U2 (RNU2) small nuclear RNA auxiliary factor 2 isoform b" [Rattus norvegicus (taxid:10116)]

 Score = 470 (170.5 bits), Expect = 2.0e-47, Sum P(2) = 2.0e-47
 Identities = 109/268 (40%), Positives = 155/268 (57%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSLPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+  +   + + G    +VLCL  M+
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMV 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0019899 "enzyme binding" evidence=IEA

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

ZFIN|ZDB-GENE-050706-131 u2af2a "U2 small nuclear RNA auxiliary factor 2a" [Danio rerio (taxid:7955)]

 Score = 468 (169.8 bits), Expect = 2.0e-47, Sum P(2) = 2.0e-47
 Identities = 109/268 (40%), Positives = 154/268 (57%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   129 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 187

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P    +  P    P  +L  V
Sbjct:   188 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPG-SLP-V 245

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   246 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 303

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  ++D A A LNG+++GDK L V+RA  S G   T                 + LQ
Sbjct:   304 EYVDVNISDQAIAGLNGMQLGDKKLLVQRA--SVGSKNT--------TLTGINQTPVTLQ 353

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+  +   ++  G    +VLCL  M+
Sbjct:   354 VPGL--MNSSVNQMGGIPTEVLCLMNMV 379

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P26368 U2AF2 "Splicing factor U2AF 65 kDa subunit" [Homo sapiens (taxid:9606)]

 Score = 469 (170.2 bits), Expect = 2.6e-47, Sum P(2) = 2.6e-47
 Identities = 109/268 (40%), Positives = 155/268 (57%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  VTD A A LNG+++GDK L V+RA+  +      + +             + LQ
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA------KNATLVSPPSTINQTPVTLQ 359

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+  +   + + G    +VLCL  M+
Sbjct:   360 VPGL--MSSQVQMGGHP-TEVLCLMNMV 384

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0070742 "C2H2 zinc finger domain binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0019899 "enzyme binding" evidence=IPI

GO:0048025 "negative regulation of mRNA splicing, via spliceosome" evidence=IDA

GO:0006397 "mRNA processing" evidence=TAS

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;TAS

GO:0005681 "spliceosomal complex" evidence=IDA

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0006369 "termination of RNA polymerase II transcription" evidence=TAS

GO:0006406 "mRNA export from nucleus" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0031124 "mRNA 3'-end processing" evidence=TAS

UNIPROTKB|E2R0G3 U2AF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 467 (169.5 bits), Expect = 4.2e-47, Sum P(2) = 4.2e-47
 Identities = 100/214 (46%), Positives = 137/214 (64%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   136 PVPVVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 194

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   
Sbjct:   195 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVP 247

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   248 GVVSTVV--PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 305

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
              Y D  VTD A A LNG+++GDK L V+RA+  +
Sbjct:   306 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 339

GO:0006397 "mRNA processing" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0005411 U2af50 "U2 small nuclear riboprotein auxiliary factor 50" [Drosophila melanogaster (taxid:7227)]

 Score = 433 (157.5 bits), Expect = 1.8e-44, Sum P(2) = 1.8e-44
 Identities = 101/248 (40%), Positives = 140/248 (56%)

Query:   134 PGVPSAVPEMAQNMLPFGATQLGAFPLMP---VQVMTQQATRHARRVYVGGLPPLANEQA 190
             PG     P   + M   G       P  P   V V+    TR ARR+YVG +P    E+ 
Sbjct:    49 PGFEHITPMQYKAMQASGQIPASVVPDTPQTAVPVVGSTITRQARRLYVGNIPFGVTEEE 108

Query:   191 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA 250
             +  FF+Q M  +G   A  G  V+   IN +K FAF+E R+++E + AMA DGI  +G +
Sbjct:   109 MMEFFNQQMHLVGLAQAA-GSPVLACQINLDKNFAFLEFRSIDETTQAMAFDGINLKGQS 167

Query:   251 VRVRRPTDYNPTLAAALGPG-QPSPNLNLAAVGLASGAIGGA--EGPDRVFVGGLPYYFT 307
             +++RRP DY P       PG   +P +  A V  +SG I     + P ++F+GGLP Y  
Sbjct:   168 LKIRRPHDYQPM------PGITDTPAIKPAVV--SSGVISTVVPDSPHKIFIGGLPNYLN 219

Query:   308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT 367
             + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D ++TD + A LNG+++GDK L 
Sbjct:   220 DDQVKELLLSFGKLRAFNLVKDAATGLSKGYAFCEYVDLSITDQSIAGLNGMQLGDKKLI 279

Query:   368 VRRATASS 375
             V+RA+  +
Sbjct:   280 VQRASVGA 287

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC;ISS;NAS;IMP

GO:0005686 "U2 snRNP" evidence=TAS

GO:0008187 "poly-pyrimidine tract binding" evidence=NAS;IDA

GO:0005681 "spliceosomal complex" evidence=ISS;NAS

GO:0000245 "spliceosomal complex assembly" evidence=NAS

GO:0046982 "protein heterodimerization activity" evidence=NAS

GO:0005634 "nucleus" evidence=IC;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051168 "nuclear export" evidence=IMP

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0007052 "mitotic spindle organization" evidence=IMP

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0008380 "RNA splicing" evidence=IMP

GO:0003723 "RNA binding" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

ZFIN|ZDB-GENE-040426-1881 u2af2b "U2 small nuclear RNA auxiliary factor 2b" [Danio rerio (taxid:7955)]

 Score = 448 (162.8 bits), Expect = 2.5e-42, P = 2.5e-42
 Identities = 109/268 (40%), Positives = 150/268 (55%)

Query:   162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
             PV V+  Q TR ARR+YVG +P    E+++  FF+  M  +GG +  PG+ V+ V IN +
Sbjct:   139 PVPVVGSQMTRQARRLYVGNIPFGITEESMMDFFNAQMR-LGGLTQAPGNPVLAVQINQD 197

Query:   222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAV 281
             K FAF+E R+V+E + AMA DGIIF+  ++++RRP DY P       PG  S N ++   
Sbjct:   198 KNFAFLEFRSVDETTQAMAFDGIIFQAQSLKIRRPHDYQPL------PGM-SENPSVYVP 250

Query:   282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G+ S  +   +   ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC
Sbjct:   251 GVVSTVV--PDSIHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 308

Query:   342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESXXXXXXXXXXXXKMALQ 401
              Y D  V D A A LNG+++ DK L V+RA  S G       S             + LQ
Sbjct:   309 EYVDVNVNDQAIAGLNGMQLADKKLLVQRA--SVGAKNATMTSINET--------PVTLQ 358

Query:   402 TSGMNTLGGGMSLFGETLAKVLCLTEMM 429
               G+ +    M   G    +VLCL  M+
Sbjct:   359 VPGLTS--NPMIQMGGIPTEVLCLMNMV 384

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0046660 "female sex differentiation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	435
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-127
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-42
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	4e-40
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-19
smart00360	73	smart00360, RRM, RNA recognition motif	5e-19
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-16
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-14
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-14
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-13
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	8e-13
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	4e-12
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-12
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	7e-12
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	8e-12
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-11
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	5e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-10
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-10
smart00360	73	smart00360, RRM, RNA recognition motif	3e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-10
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-10
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-10
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	5e-10
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	8e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-09
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	4e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-09
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	6e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-08
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	3e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	3e-08
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	4e-08
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-08
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	7e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-07
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-07
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-07
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-07
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-07
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	4e-07
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-07
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	5e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	6e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	7e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	7e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-07
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	8e-07
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-07
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-06
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-06
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	5e-06
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	6e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	8e-06
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	9e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	1e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-05
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	1e-05
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-05
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-05
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	2e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	2e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-05
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	4e-05
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	4e-05
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	4e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	4e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	4e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	4e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-05
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	5e-05
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	5e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	5e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	5e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	7e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	8e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	8e-05
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	8e-05
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	8e-05
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	8e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	9e-05
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	1e-04
pfam08648	158	pfam08648, DUF1777, Protein of unknown function (D	1e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-04
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	1e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	1e-04
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-04
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-04
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-04
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	4e-04
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-04
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-04
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	4e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	4e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-04
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
cd12439	79	cd12439, RRM_TRMT2A, RNA recognition motif in tRNA	5e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	6e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	6e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	7e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	7e-04
pfam12871	97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	0.001
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.001
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	0.001
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	0.001
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.001
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	0.001
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.002
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.003
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.003
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.003
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.003
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.003
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.003
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.003
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.004
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.004
cd12299	71	cd12299, RRM4_Prp24, RNA recognition motif 4 in fu	0.004

>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor

 Score =  377 bits (969), Expect = e-127
 Identities = 158/413 (38%), Positives = 207/413 (50%), Gaps = 29/413 (7%)

Query: 25  RSRTGERGRDRHHR--DFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           RSR   R RDRH R  +     D R RD+  +YD    R    +   R        R R 
Sbjct: 27  RSRDRSRFRDRHRRSRERSYREDSRPRDR-RRYDSRSPRSLRYSSVRRS-------RDRP 78

Query: 83  RSRSHSSDRF---RNRSKSLSPSRSPSKS-KRRSGFDMAPPA-AAMLPGAAVPGQLPGVP 137
           R RS S       R R +  SPS    K  K+RS +D+ PP    +    A   Q+  VP
Sbjct: 79  RRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIKPPGYELVTADQAKASQVFSVP 138

Query: 138 SAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ 197
              P  A         +      +PV    QQATR ARR+YVGG+PP   E+A+  FF+ 
Sbjct: 139 GTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQATRQARRLYVGGIPPEFVEEAVVDFFND 198

Query: 198 VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           +M A G + A  G  V +V IN EK FAF+E RTVEEA+ AMALD II+  V +++RRP 
Sbjct: 199 LMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPH 258

Query: 258 DYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLES 317
           DY P         Q +P+ N   V     +    +  DR+++G LP Y  E QIKELLES
Sbjct: 259 DYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLES 318

Query: 318 FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ 377
           FG L  F+L+KD  TG SKGY FC Y+DP+VTD+A AALNG   GD  L V+RA   + Q
Sbjct: 319 FGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQ 378

Query: 378 SKTEQESILAQ-AQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMM 429
           +  +  + +A       A+ +  LQ              G    KV+ LT ++
Sbjct: 379 ATIDTSNGMAPVTLLAKALSQSILQI-------------GGKPTKVVQLTNLV 418

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score =  144 bits (366), Expect = 1e-42
 Identities = 49/77 (63%), Positives = 61/77 (79%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           +++F+GGLP Y +E Q+KELLESFG L  F+LVKD  TG SKGY FC Y DP+VTD A A
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 355 ALNGLKMGDKTLTVRRA 371
            LNG+++GDK LTV+RA
Sbjct: 61  GLNGMQLGDKKLTVQRA 77

This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 77

>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score =  137 bits (348), Expect = 4e-40
 Identities = 48/83 (57%), Positives = 61/83 (73%), Gaps = 1/83 (1%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG LPP   E+ +  FF+Q M A G N   PG+ V++V IN EK FAFVE RTVE
Sbjct: 1   ARRLYVGNLPPGITEEELVDFFNQAMLAAGLN-QAPGNPVLSVQINPEKNFAFVEFRTVE 59

Query: 234 EASNAMALDGIIFEGVAVRVRRP 256
           EA+ A+ALDGIIF+G  +++RRP
Sbjct: 60  EATAALALDGIIFKGQPLKIRRP 82

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 90.0 bits (223), Expect = 2e-19
 Identities = 87/379 (22%), Positives = 128/379 (33%), Gaps = 100/379 (26%)

Query: 25  RSRTGERGRDRHHRDFKSGGDDRRRDK--NYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
           R R  ERGR    R+     D RR DK       R   RD  R  R RDY R +  R R 
Sbjct: 1   RYRDRERGR---LRN-----DTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRS 52

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPPAAAMLPGAAVPGQLPGVPSAVPE 142
           RS +        R +     R   +   R+                              
Sbjct: 53  RSPNR-----YYRPRGDRSYRRDDRRSGRN------------------------------ 77

Query: 143 MAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI 202
                                + +T+ A R  R V+V  L   A E+ +  FFS+V    
Sbjct: 78  -------------------TKEPLTE-AERDDRTVFVLQLALKARERDLYEFFSKV---- 113

Query: 203 GGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRP 256
                G    V +V           K  A+VE   VE    A+AL G +  G  + V+  
Sbjct: 114 -----GK---VRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQ-S 164

Query: 257 TDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE 316
           +      AA     QP                G      +++VG L +  TE +++++ E
Sbjct: 165 SQAEKNRAAKAATHQP----------------GDIPNFLKLYVGNLHFNITEQELRQIFE 208

Query: 317 SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG 376
            FG +    L +D +TG SKG+GF  + D      A   +NG ++  + + V  A  S+ 
Sbjct: 209 PFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTY 268

Query: 377 QSKTEQESILAQAQQHIAI 395
                        QQ +  
Sbjct: 269 LLDAANTFEDIDKQQQMGK 287

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 80.3 bits (199), Expect = 5e-19
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG LP   TE +++EL   FG +    LV+D++TG SKG+ F  ++     + A  A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 356 LNGLKMGDKTLTV 368
           LNG ++  + L V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 73.0 bits (180), Expect = 3e-16
 Identities = 32/72 (44%), Positives = 40/72 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+ E+    G +  F LV DRDTG  KGYGFC ++D      A   L
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 357 NGLKMGDKTLTV 368
           NG +   + L V
Sbjct: 61  NGYEFNGRALRV 72

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 71.6 bits (176), Expect = 7e-16
 Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG LP   TE  ++EL   FG +    +V+D+D G SKG+ F  ++ P   + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 357 NGLKMGDKTLTVR 369
           NG ++  + L V 
Sbjct: 60  NGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 70.6 bits (173), Expect = 2e-15
 Identities = 33/75 (44%), Positives = 43/75 (57%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC Y+D      A   L
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 357 NGLKMGDKTLTVRRA 371
           NG ++  + L V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG LP   TE  +K+L   FG +    +V+D  TG SKG+ F  ++D    + A  AL
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 357 NGLKMGDKTLT 367
           NG ++G + L 
Sbjct: 60  NGKELGGRELR 70

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 28/72 (38%), Positives = 44/72 (61%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++GGLPY  TE  I  +   +G +   +LV+D+ TG SKG+ F  Y+D   T +A   L
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 357 NGLKMGDKTLTV 368
           NG+K+  +T+ V
Sbjct: 72  NGIKLLGRTIRV 83

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 29/76 (38%), Positives = 42/76 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG LPY  TE  +K+L   FG +    ++ DR+TG S+G+GF   +     + A   
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG   G +TLTV  A
Sbjct: 61  LNGTDFGGRTLTVNEA 76

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 64.5 bits (158), Expect = 3e-13
 Identities = 22/73 (30%), Positives = 39/73 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++G LP+ F E ++++    FGT+    L + + TG SKGY F  ++ P V  I    +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 357 NGLKMGDKTLTVR 369
           N   + ++ L  +
Sbjct: 62  NNYLLFERLLKCK 74

This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 74

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 69.2 bits (168), Expect = 4e-13
 Identities = 33/111 (29%), Positives = 56/111 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG LPY  TE  ++EL + FG +    LV+DR+TG S+G+ F  ++     + A   
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMN 406
           LNG ++  + L V++A  +S        ++ A   + ++  K  L     N
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDN 227

Length = 306

>gnl|CDD|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 63.3 bits (154), Expect = 8e-13
 Identities = 25/73 (34%), Positives = 41/73 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++G LP+ F E ++K+    FGT+    + + + TGNSK YGF  + +P V  IA  ++
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 357 NGLKMGDKTLTVR 369
           N   +  K L V 
Sbjct: 62  NNYLLMGKVLQVH 74

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 25/67 (37%), Positives = 36/67 (53%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +++ L E+ G +    +V+DR TG S GYGF  Y D      A   LNG ++
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 362 GDKTLTV 368
            +K L V
Sbjct: 68  RNKRLKV 74

This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 77

>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 30/75 (40%), Positives = 38/75 (50%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
            VG LP  FT+ Q +EL+  FG +    LV    TG SKGYGF  Y   A    A   L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 358 GLKMGDKTLTVRRAT 372
           G ++G + L V  A 
Sbjct: 63  GKQIGGRKLQVDWAD 77

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 60.9 bits (148), Expect = 5e-12
 Identities = 28/70 (40%), Positives = 40/70 (57%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +I+ L  S G +    L++D+ TG S GYGF  Y DP   + A   LNGL++
Sbjct: 9   LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRL 68

Query: 362 GDKTLTVRRA 371
            +KT+ V  A
Sbjct: 69  QNKTIKVSYA 78

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 60.7 bits (148), Expect = 7e-12
 Identities = 30/73 (41%), Positives = 42/73 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +P   ++  I++LLE  G +  +  VKD  TG  K +GFC ++DP     A   
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRL 61

Query: 356 LNGLKMGDKTLTV 368
           LNGL++G K L V
Sbjct: 62  LNGLELGGKKLLV 74

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 60.5 bits (146), Expect = 8e-12
 Identities = 34/79 (43%), Positives = 42/79 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 357 NGLKMGDKTLTVRRATASS 375
           NGLK+  KT+ V  A  SS
Sbjct: 66  NGLKLQTKTIKVSYARPSS 84

This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 26/76 (34%), Positives = 41/76 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R++V  +    +E  IK + E+FG +    L  D +TG  KGYGF  Y++P     A A+
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 356 LNGLKMGDKTLTVRRA 371
           +N   +G + L V +A
Sbjct: 62  MNLFDLGGQQLRVGKA 77

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240776 cd12330, RRM2_Hrp1p, RNA recognition motif 2 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 58.2 bits (141), Expect = 5e-11
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLP   TE + KE    FG +    L++D DTG S+G+GF  +   +  +   +A
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 356 LNGLKMGDKTLTVRRA 371
              L++G K + V+RA
Sbjct: 61  -GMLELGGKQVEVKRA 75

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 75

>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 57.7 bits (140), Expect = 7e-11
 Identities = 24/71 (33%), Positives = 37/71 (52%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           +VG L +  TE  ++ + E FG +    L +D +TG SKGYGF  + D      A   LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 358 GLKMGDKTLTV 368
           G ++  + + V
Sbjct: 62  GFELAGRPIKV 72

This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. . Length = 73

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P+R+FVGG+P   TE ++++    FG++    ++ DR  G SKGYGF  ++     +   
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKIL 60

Query: 354 AALNGLKMGDKTLTVRRA 371
           A  N L    K L +  A
Sbjct: 61  AMGN-LNFRGKKLNIGPA 77

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 25/79 (31%), Positives = 43/79 (54%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            +++FV GL    TE +++ L   FG +    L+KD +TG S+G+GF  ++     D A 
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAI 60

Query: 354 AALNGLKMGDKTLTVRRAT 372
             LNG ++  + + V +A 
Sbjct: 61  RDLNGKELEGRVIKVEKAK 79

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|214636 smart00360, RRM, RNA recognition motif

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            ++VG LPP   E+ +   FS+          G    V +V +  +K+      FAFVE 
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKF---------GK---VESVRLVRDKETGKSKGFAFVEF 48

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
            + E+A  A+ AL+G   +G  ++V
Sbjct: 49  ESEEDAEKALEALNGKELDGRPLKV 73

Length = 73

>gnl|CDD|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins

 Score = 56.0 bits (135), Expect = 3e-10
 Identities = 23/79 (29%), Positives = 45/79 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++P     A  A
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 356 LNGLKMGDKTLTVRRATAS 374
           +NG  +  + + V +A  S
Sbjct: 62  MNGKSVDGRQIRVDQAGKS 80

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

>gnl|CDD|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 56.3 bits (135), Expect = 3e-10
 Identities = 31/79 (39%), Positives = 42/79 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 357 NGLKMGDKTLTVRRATASS 375
           NGL++  KT+ V  A  SS
Sbjct: 65  NGLRLQTKTIKVSYARPSS 83

This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 56.3 bits (135), Expect = 3e-10
 Identities = 30/75 (40%), Positives = 41/75 (54%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ ++K L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 357 NGLKMGDKTLTVRRA 371
           NGL++  KT+ V  A
Sbjct: 67  NGLRLQTKTIKVSYA 81

This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 83

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 60.3 bits (146), Expect = 5e-10
 Identities = 31/78 (39%), Positives = 43/78 (55%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ +I+ L  S G +    LV+D+ TG S GYGF  Y  P   + A  +LNGL++
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 362 GDKTLTVRRATASSGQSK 379
            +KT+ V  A  SS   K
Sbjct: 71  QNKTIKVSYARPSSDSIK 88

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 55.1 bits (133), Expect = 5e-10
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VGG+PYY TE +I+      G +   DL+   DTG  +G  F  ++       A  AL
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRA-LAL 59

Query: 357 NGLKMGDKTLTVR 369
           +G  MG + L V 
Sbjct: 60  DGEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           F+GGL +  TE  ++E    +G +    ++KD  TG S+G+GF  + DP+  D   AA
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAA 59

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 18/84 (21%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRT 231
           ++VG LPP   E+ +   FS+          G    + +V I        K FAFVE  +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKF---------GE---IESVRIVRDKDGKSKGFAFVEFES 48

Query: 232 VEEASNAM-ALDGIIFEGVAVRVR 254
            E+A  A+ AL+G   +G  ++V 
Sbjct: 49  PEDAEKALEALNGKELDGRKLKVS 72

RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). Length = 72

>gnl|CDD|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 5/80 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF+  LP+  TE ++KEL   FG +    +VKD+ TG+SKG  F  ++          A 
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 357 N-----GLKMGDKTLTVRRA 371
           +     GL +  + L V  A
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 82

>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 20/75 (26%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++FV GLP+  T+ ++++L +  G +    LV +R +G  KG  +  Y++ +    A 
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAV 60

Query: 354 AALNGLKMGDKTLTV 368
             ++G ++ +KT++V
Sbjct: 61  LKMDGTEIKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 57.3 bits (137), Expect = 4e-09
 Identities = 40/187 (21%), Positives = 69/187 (36%), Gaps = 24/187 (12%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
                  Q++      ++VG LP    E+ +   F +               V  V +  
Sbjct: 102 SESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGP------------VKRVRLVR 149

Query: 221 EKK------FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
           +++      FAFVE  + E A  A+  L+G   EG  +RV++    +   +        +
Sbjct: 150 DRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSEL-----SN 204

Query: 274 PNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
                 A  L+ G     E  D ++VG LP    E ++ +L +S G +    L   +D  
Sbjct: 205 NLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK 264

Query: 334 NSKGYGF 340
             K   F
Sbjct: 265 IPKSRSF 271

Length = 306

>gnl|CDD|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 52.9 bits (128), Expect = 4e-09
 Identities = 22/63 (34%), Positives = 34/63 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG LP   TE  ++ L E +G +    +++D+DTG SKG  F  +        A  A
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 356 LNG 358
           L+G
Sbjct: 61  LHG 63

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 52.7 bits (127), Expect = 4e-09
 Identities = 23/63 (36%), Positives = 36/63 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV  LP+  TE +++EL E+FG +    L  D++T  SKG+ F  +  P     A + 
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 356 LNG 358
           L+G
Sbjct: 61  LDG 63

This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 74

>gnl|CDD|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG LP+   E ++++  E  G +    +V+DR TG  KG+G+ +++      +A   L
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KL 60

Query: 357 NGLKMGDKTLTV 368
           NG+K+  + + V
Sbjct: 61  NGIKLKGRKIRV 72

This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 73

>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 23/62 (37%), Positives = 37/62 (59%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++    FG +    ++ DR TG S+GYGF  ++D    + AC  
Sbjct: 2   KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 356 LN 357
            N
Sbjct: 62  PN 63

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+V  L     + ++KEL   +G +    ++KD D G SKG+GF  +++      A   L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 357 NGLKMGDKTLTVRRA 371
           NG ++  K L V RA
Sbjct: 63  NGKEVNGKKLYVGRA 77

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

>gnl|CDD|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 21/63 (33%), Positives = 36/63 (57%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG L +   +  +K   E FGT+ G  ++ DR+TG S+G+G+  ++ P     A  A
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 356 LNG 358
           ++G
Sbjct: 61  MDG 63

This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 76

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 13/79 (16%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           VYVG LP    E+ +   FS            P  A+  V +  +K +AFV   T E A+
Sbjct: 3   VYVGNLPHGLTEEELQRTFS------------PFGAIEEVRVFKDKGYAFVRFDTHEAAA 50

Query: 237 NAM-ALDGIIFEGVAVRVR 254
            A+ A++G    G  V+  
Sbjct: 51  TAIVAVNGTSINGQTVKCS 69

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 293 GPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           GP+   +F+  LP  F + ++ ++   FG +    +  DR T  SK +GF  + +PA   
Sbjct: 1   GPEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQ 60

Query: 351 IACAALNGLKMGDKTLTVR 369
            A  A+NG ++G K L V+
Sbjct: 61  AAIQAMNGFQIGMKRLKVQ 79

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 50.1 bits (119), Expect = 3e-08
 Identities = 26/78 (33%), Positives = 41/78 (52%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y +    + A   L
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 357 NGLKMGDKTLTVRRATAS 374
           NGL++  KT+ V  A  S
Sbjct: 64  NGLRLQSKTIKVSYARPS 81

This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 81

>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 18/78 (23%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMRT 231
           ++VG LPP   E+ +   FS+          GP   + ++ I  +     K FAFVE   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKF---------GP---IESIRIVRDETGRSKGFAFVEFED 48

Query: 232 VEEASNAM-ALDGIIFEG 248
            E+A  A+ AL+G    G
Sbjct: 49  EEDAEKALEALNGKELGG 66

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. Length = 70

>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint family

 Score = 55.1 bits (132), Expect = 4e-08
 Identities = 53/212 (25%), Positives = 84/212 (39%), Gaps = 31/212 (14%)

Query: 164 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INH 220
           Q   QQA     RVYVG +     E  I   F            GP  ++   +      
Sbjct: 97  QQQRQQALAIMCRVYVGSISFELREDTIRRAFDPF---------GPIKSINMSWDPATGK 147

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLA 279
            K FAFVE    E A  A+  ++G +  G  ++V RP++            Q  P +++ 
Sbjct: 148 HKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM----------PQAQPIIDMV 197

Query: 280 AVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
                      A+  +R++V  +    +ET IK + E+FG +    L +       KGYG
Sbjct: 198 Q--------EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYG 249

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           F  Y +      A A++N   +G + L V + 
Sbjct: 250 FIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC 281

The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. Length = 612

>gnl|CDD|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 17/60 (28%), Positives = 30/60 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    TE  ++E    +G +   ++V D++TG  +G+ F  + D    D     
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 49.1 bits (117), Expect = 7e-08
 Identities = 25/71 (35%), Positives = 36/71 (50%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           V  LP  FT  + +EL+ ++G +    LV    TG+SKGYGF  Y        A   L G
Sbjct: 4   VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELLG 63

Query: 359 LKMGDKTLTVR 369
            ++G+ TL  +
Sbjct: 64  KQLGESTLFAQ 74

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 22/67 (32%), Positives = 35/67 (52%)

Query: 302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM 361
           LP   T+ + + L  + G +    +V+D+ TG S G+GF  YQ       A   LNGL++
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 362 GDKTLTV 368
            +K + V
Sbjct: 68  QNKRIKV 74

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

>gnl|CDD|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 19/75 (25%), Positives = 33/75 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LPY  T+ Q++E     G +    +VKD+ +   +G+G+  +        A    
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 357 NGLKMGDKTLTVRRA 371
              K G + + V  A
Sbjct: 62  KKTKFGGRKIHVEFA 76

This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 79

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 13/80 (16%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           R++VG LP    E+     FS+            G+ V  V++N EK F F+ + T   A
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKY-----------GE-VSEVFLNKEKGFGFIRLDTRTNA 50

Query: 236 SNA-MALDGIIFEGVAVRVR 254
             A   LDGI+ +G  +RVR
Sbjct: 51  EKAKAELDGIMRKGRQLRVR 70

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 25/72 (34%), Positives = 39/72 (54%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +F+  LP  FT+  + +L   FG +    +  D++TG SK +GF  Y +P     A  A+
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 357 NGLKMGDKTLTV 368
           NG ++G K L V
Sbjct: 61  NGFQVGGKRLKV 72

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

>gnl|CDD|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G EG + +F+  LP  FT+T + +    FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 1   GPEGCN-LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSA 59

Query: 350 DIACAALNGLKMGDKTLTVR 369
             A  A+NG ++G K L V+
Sbjct: 60  QAAIQAMNGFQIGTKRLKVQ 79

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 22/75 (29%), Positives = 37/75 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV+VG + +   E  I++    FG +   D+  D  T   KG+ F  Y+ P    +A   
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ 61

Query: 356 LNGLKMGDKTLTVRR 370
           +NG+ +G + + V R
Sbjct: 62  MNGVMLGGRNIKVGR 76

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L    TE  + EL    G L G  + KD + G  K + F  ++       A   L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 357 NGLKMGDKTLTVR 369
           NG+++  + L ++
Sbjct: 63  NGIRLFGRELRIK 75

This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 47.6 bits (113), Expect = 2e-07
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +F+GGL +  T+  ++E    FG +    +++D  TG S+G+GF  ++ P   + 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNE 55

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 25/84 (29%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRT 231
            +YVG LP    E+ +   F Q                  V  + E    + F FVEM T
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTS----------ARVITDRETGRSRGFGFVEMET 50

Query: 232 VEEASNAM-ALDGIIFEGVAVRVR 254
            EEA+ A+  L+G  F G  + V 
Sbjct: 51  AEEANAAIEKLNGTDFGGRTLTVN 74

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 47.3 bits (112), Expect = 4e-07
 Identities = 27/70 (38%), Positives = 37/70 (52%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           +  LP  +T+ Q +EL+  FG L    LV    TG+SKGYGF  Y        A + L G
Sbjct: 4   IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLLG 63

Query: 359 LKMGDKTLTV 368
            ++G +TL V
Sbjct: 64  KQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P+R+FVGG+ +   E  +++    +GT+    +V DR  G SKGYGF  ++         
Sbjct: 2   PNRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKIL 60

Query: 354 AALNGLKMGDKTLTVRRA 371
              N L   DK L + +A
Sbjct: 61  QEANRLCFRDKKLNIGQA 78

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + D
Sbjct: 5   PNTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYD 55

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

>gnl|CDD|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 20/50 (40%), Positives = 27/50 (54%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           V GLP+  TE  +K+   +FG L    + KD  TG SKG+GF  + D   
Sbjct: 4   VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYED 53

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV  LPY   E  +++L   FG L    +  D+ +G SKG+ + ++ DP   + A  A
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDP---EDAVKA 60

Query: 356 LNGL 359
              L
Sbjct: 61  YKEL 64

This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 79

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 46.4 bits (111), Expect = 7e-07
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   +F+  L        + +   +FG +    +  D + G SKGYGF  ++       A
Sbjct: 1   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRA 59

Query: 353 CAALNGLKMGDKTLTV 368
              +NG+ + DK + V
Sbjct: 60  IEKVNGMLLNDKKVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

>gnl|CDD|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 46.2 bits (110), Expect = 7e-07
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLP   TET +++    FGT+    ++ D +    +G+GF  ++     D     
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVV-N 62

Query: 356 LNGLKMGDKTLTVRRA 371
            +   +  K + V+RA
Sbjct: 63  EHFHDINGKKVEVKRA 78

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 46.0 bits (110), Expect = 8e-07
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK----KFAFVEMRTV 232
           +YV  LPP   E+ +  FFS            P   V  V +   K     FAFVE  + 
Sbjct: 1   LYVRNLPPSVTEEDLREFFS------------PYGKVEGVRLVRNKDRPRGFAFVEFASP 48

Query: 233 EEASNAMA-LDGIIFEG 248
           E+A  A+  L+G++ +G
Sbjct: 49  EDAEAALKKLNGLVLDG 65

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 46.0 bits (110), Expect = 8e-07
 Identities = 23/74 (31%), Positives = 34/74 (45%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VG L    TE  + EL    G +    + KDR T   +GYGF  +      D A   +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 357 NGLKMGDKTLTVRR 370
           N +K+  K + V +
Sbjct: 61  NMIKLYGKPIRVNK 74

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 46.2 bits (110), Expect = 9e-07
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV---YQDPAVTDIAC 353
           +FV  LP    E+ + +L   FG +    +++D  T   KGYGF     Y++      A 
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYS---AI 60

Query: 354 AALNGLKMGDKTLTV 368
           A+LNG ++G + L V
Sbjct: 61  ASLNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  LP   TE  ++E    +G + G  LV+++D    +G+ F  +  P   + A   L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 357 NGLKMGDKTL 366
           NGL +  +TL
Sbjct: 59  NGLVLDGRTL 68

k.a. RRM, RBD, or RNP domain). Length = 69

>gnl|CDD|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +F+G L     E  + +   +FG  L    +++D DTGNSKG+ F  Y     +D A  A
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG  + ++ +TV  A
Sbjct: 64  MNGQYLCNRPITVSYA 79

This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 83

>gnl|CDD|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.5 bits (108), Expect = 2e-06
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIAC 353
           R+F+  L Y  TE  +++L   +G L    L  D+ T   KG+ F  Y  P  AV   A 
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVK--AF 61

Query: 354 AALNG 358
           A L+G
Sbjct: 62  AELDG 66

This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+ V  LP Y TE +++E  ES G +    +++ RD G S+ +GF  ++       A   
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQAVKY 60

Query: 356 LNGLKMGDKTLTVRRA 371
            N   +    ++V  A
Sbjct: 61  FNKTFIDTSKISVELA 76

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 20/64 (31%), Positives = 31/64 (48%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ GLP   T+  +++L + FG +     + D+ T   KGYGF  +  P     A   L
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGL 62

Query: 357 NGLK 360
           NG  
Sbjct: 63  NGRG 66

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

>gnl|CDD|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 21/75 (28%), Positives = 36/75 (48%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+V  LP+  T   + ++   +G +    +VKD++T  SKG  F ++ D         AL
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 357 NGLKMGDKTLTVRRA 371
           N  ++  +TL    A
Sbjct: 64  NNKELFGRTLKCSIA 78

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 16/45 (35%), Positives = 28/45 (62%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           R+FVGGL    TE+ ++E    FGT+   +++K +D G  +G+ +
Sbjct: 1   RLFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAY 45

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + +L   FG ++   +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 357 NGLKMGDKTLTVRRAT 372
           NG ++GD+ L V   T
Sbjct: 66  NGYRLGDRVLQVSFKT 81

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 44.2 bits (105), Expect = 6e-06
 Identities = 20/71 (28%), Positives = 35/71 (49%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           FV  L Y  TE++++   E +G +    LV+D+ TG  +GY F  ++       A    +
Sbjct: 5   FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 358 GLKMGDKTLTV 368
           G K+  + + V
Sbjct: 65  GKKIDGRRVLV 75

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           R+FV  +P  +TE  ++E  + FG +    +VKD++TG SKG+G+  +  P+   +A
Sbjct: 3   RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVA 58

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 294 PD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           PD  ++FVG LP+  TE ++KE  + FG +    +      G    +GF V+ DP     
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 352 ACAALNGLKMGDKTLTV 368
             A       GD  L V
Sbjct: 61  ILANKPIYFRGDHRLNV 77

This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). Length = 81

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 43.9 bits (103), Expect = 8e-06
 Identities = 25/80 (31%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 292 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF  Y +P   
Sbjct: 3   EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62

Query: 350 DIACAALNGLKMGDKTLTVR 369
             A  A+NG ++G K L V+
Sbjct: 63  QAAIQAMNGFQIGMKRLKVQ 82

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 43.4 bits (102), Expect = 9e-06
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V + AC  
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVRFESPEVAERACRM 58

Query: 356 LNGLKMGDKTLTVR 369
           +NG K+  + + VR
Sbjct: 59  MNGYKLNGREIDVR 72

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 46.9 bits (111), Expect = 1e-05
 Identities = 27/103 (26%), Positives = 42/103 (40%), Gaps = 6/103 (5%)

Query: 272 PSPNLNLAAVGLASGAIGGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFD 325
                  A  G  +G   GA+          +FV  L     ET + +L   FG +    
Sbjct: 241 AQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVK 300

Query: 326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV 368
           +++D  T   KGYGF    +     +A  +LNG  +G++ L V
Sbjct: 301 IIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE + KEL   +G +    L K+      KG+GF         + A A 
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+G+    + L VR
Sbjct: 57  LDGIMRKGRQLRVR 70

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

>gnl|CDD|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 21/70 (30%), Positives = 33/70 (47%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L        ++     FG +    +VKD  TG SKGYGF  +      + A  ++
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 357 NGLKMGDKTL 366
           NG  +G + +
Sbjct: 62  NGQWLGGRAI 71

This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 75

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 22/79 (27%), Positives = 40/79 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 357 NGLKMGDKTLTVRRATASS 375
           NG ++GD+ L V   T  +
Sbjct: 66  NGYRLGDRVLQVSFKTNKT 84

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241022 cd12578, RRM1_hnRNPA_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL Y  T+  +K     +G +    ++KD +T  S+G+GF  +   +  D A  A
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 356 LNGLKMGDKTLTVRRATA 373
               K+  + +  +RA  
Sbjct: 61  -RPHKVDGREVEPKRAVP 77

This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 78

>gnl|CDD|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 23/79 (29%), Positives = 40/79 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +F+  L     E  + ++   FG +    +++D +T   KG+GF    +     +A A+L
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 357 NGLKMGDKTLTVRRATASS 375
           NG ++GDK L V   T+ S
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

>gnl|CDD|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.0 bits (101), Expect = 1e-05
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           ++FVGGL     E  + E    FG +   +++ D+ TG  +G+GF  +Q+    D A
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 17/85 (20%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-----KKFAFVEMR 230
           R++VGG+PP   E+ +  FFS+              +V +V I  +     K + FV   
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRF------------GSVKDVKIITDRAGVSKGYGFVTFE 51

Query: 231 TVEEASNAMALDGIIFEGVAVRVRR 255
           T E+A   +A+  + F G  + +  
Sbjct: 52  TQEDAEKILAMGNLNFRGKKLNIGP 76

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           VYVG L     E+ +   F Q         AGP   VVNV+I         + + FVE  
Sbjct: 1   VYVGNLDEKVTEELLWELFIQ---------AGP---VVNVHIPKDRVTQAHQGYGFVEFL 48

Query: 231 TVEEASNAMA-LDGIIFEGVAVRVRR 255
           + E+A  A+  ++ I   G  +RV +
Sbjct: 49  SEEDADYAIKIMNMIKLYGKPIRVNK 74

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240688 cd12242, RRM_SLIRP, RNA recognition motif found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins

 Score = 42.3 bits (100), Expect = 2e-05
 Identities = 18/51 (35%), Positives = 29/51 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           ++FVG LP+     ++KE    FG +   ++  D++TG SKGYGF  +   
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. . Length = 73

>gnl|CDD|241076 cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 42.8 bits (101), Expect = 2e-05
 Identities = 21/65 (32%), Positives = 33/65 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG +P    E  ++ L E FG ++   ++KD+ TG  KG  F  Y        A +A
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 356 LNGLK 360
           L+  K
Sbjct: 67  LHEQK 71

This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 87

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 14/55 (25%), Positives = 30/55 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++FVGG+     E  +++  E +G +   ++++DR +G  +G+ F  + D    D
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVD 56

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VGGL     E  +      FG +    +  D +T   +G+ F  +++P   + A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAAI 57

Query: 357 ---NGLKMGDKTLTV 368
              N  ++  +T+ V
Sbjct: 58  DNMNESELFGRTIRV 72

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L Y     ++KE+ +  G +   D+ +D++ G S+G G   ++ P     A +  
Sbjct: 1   IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAISMF 59

Query: 357 NGLKMGDKTLTVR 369
           NG  + D+ + V+
Sbjct: 60  NGQMLFDRPMRVK 72

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins

 Score = 42.1 bits (100), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 307 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
            E  ++EL   FG +    L KD++TG S+G+ F  +      + A   LNG
Sbjct: 12  DEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE   K+L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+G  + ++ L +R
Sbjct: 57  LDGTILKNRPLRIR 70

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMR 230
           R ++VGG+    +E  +  FFS      G         V  V +     H  +FAFVE  
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFS----NCG--------EVTRVRLCGDRQHSARFAFVEFA 48

Query: 231 TVEEASNAMALDGIIFEGVAVRV 253
             E A +A+ L G +  G  +RV
Sbjct: 49  DAESALSALNLSGTLLGGHPLRV 71

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 8/76 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV++G LPY   E  ++   + +G +        R+     G+GF  ++DP   D A   
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG ++  + + V  A
Sbjct: 53  LNGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL    TE  +K+    FG +    L+ D+ T   +G+GF  ++   V D  C
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVC 58

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 18/69 (26%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGP-GDAV-VNVYINHEKK----FAFVEMR 230
           +YVGGL    +E+ +   F             P GD   + + +++E +    FAFVE  
Sbjct: 1   LYVGGLAEEVDEKVLHAAFI------------PFGDIKDIQIPLDYETQKHRGFAFVEFE 48

Query: 231 TVEEASNAM 239
             E+A+ A+
Sbjct: 49  EPEDAAAAI 57

This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. . Length = 73

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 43.3 bits (102), Expect = 4e-05
 Identities = 33/92 (35%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 23  SGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKE----R 78
             RSR+  R R R  R       +RRR++     R   RD  R  R R  +R +     R
Sbjct: 3   RSRSRSPRRSR-RRGRSRSRDRRERRRER----SRSRERDRRRRSRSRSPHRSRRSRSPR 57

Query: 79  RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKR 110
           RHR RSRS S  R R R +    +R P K +R
Sbjct: 58  RHRSRSRSPSRRRDRKRERD-KDAREPKKRER 88

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 42.1 bits (99), Expect = 4e-05
 Identities = 23/63 (36%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 29 GERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHS 88
          G R   R  R         R+ +  + DR+  R  DR DR RD       R R RSRS S
Sbjct: 36 GRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRDRDR----YDRSRSRSRSRS 91

Query: 89 SDR 91
           DR
Sbjct: 92 RDR 94

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LPY  TE  +      FG++     V D+ TG +KG GF  ++D    +   A L
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN---ACL 60

Query: 357 NGLKMGDKTLTV 368
                   T  +
Sbjct: 61  KNAPAAGSTSLL 72

This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 107

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG--YGFCVYQDPAVTDIACA 354
           ++VG L    TE  +K++ +  G +    ++ D+   N+KG  YGF  Y      +IA  
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK---NNKGVNYGFVEYHQSHDAEIALQ 57

Query: 355 ALNGLKMGDKTLTVRRA 371
            LNG ++ +  + V  A
Sbjct: 58  TLNGRQIENNEIRVNWA 74

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 16/55 (29%), Positives = 33/55 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++FVGGL +  ++  +K+    FG +    +  D +TG S+G+GF +++D +  +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVE 55

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 21/50 (42%), Positives = 27/50 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           +VFVGGL    TE QIKE   +FG +   +L  D  T   +G+ F  Y D
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTD 50

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 23/82 (28%), Positives = 41/82 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L     E+ + +L   FG +    +++D  T   KG+GF    +     +A A+L
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 357 NGLKMGDKTLTVRRATASSGQS 378
           NG ++GD+ L V   T+   ++
Sbjct: 64  NGYRLGDRVLQVSFKTSKQHKA 85

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

 Score = 41.2 bits (97), Expect = 4e-05
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+ V  +P+ F +  ++++   FG +   +++  +R    SKG+GF  + + A  D A  
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNER---GSKGFGFVTFANSADADRARE 58

Query: 355 ALNGLKMGDKTLTVRRAT 372
            L+G  +  + + V  AT
Sbjct: 59  KLHGTVVEGRKIEVNNAT 76

This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 19/86 (22%), Positives = 26/86 (30%), Gaps = 1/86 (1%)

Query: 21  WVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRH 80
                    +    R        G    R +  +  R   R   R  R RD +R + R  
Sbjct: 13  EEESEEEEDDEEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDR 72

Query: 81  RHRSRSHSSDRFRNRSKSLSPSRSPS 106
             R R       R+RS+S S  R   
Sbjct: 73  DDRDRDRYDRS-RSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF  GL  Y TE  ++E+   +G +    +V D+ TG S+G+GF  ++       A   L
Sbjct: 4   VF--GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERL 61

Query: 357 NGLKMGDKTLTV 368
           NG+++  + + V
Sbjct: 62  NGMEIDGRRIRV 73

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 41.1 bits (96), Expect = 5e-05
 Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 295 DR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           DR +FVG L     E  + EL    G L    + KD++ G  K +GF  ++       A 
Sbjct: 1   DRTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAI 59

Query: 354 AALNGLKMGDKTLTVR 369
           A LNG+++  + + V 
Sbjct: 60  ALLNGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 357 NGLKMGDKTLTVRRAT 372
            G  +G + +    AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 40.9 bits (96), Expect = 5e-05
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ G  P  F  + +K L E+ G +    ++          + F  +++     +A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIET 56

Query: 356 LNGLKMGDKTLTVRR 370
           LNG  +    + V+R
Sbjct: 57  LNGASVDGNCIKVQR 71

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

>gnl|CDD|240683 cd12237, RRM_snRNP35, RNA recognition motif found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           +FVG L    TE  ++E+   +G +    LV+D  TG SKGY F  Y+ 
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEH 54

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 40.8 bits (95), Expect = 7e-05
 Identities = 26/76 (34%), Positives = 35/76 (46%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 357 NGLKMGDKTLTVRRAT 372
            G  +G + +    AT
Sbjct: 64  GGQWLGGRQIRTNWAT 79

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

>gnl|CDD|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 19/72 (26%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG + Y  T  +++E  +S GT++   ++ D+ TG  KG+ +  + D +  + A   L
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENAL-LL 60

Query: 357 NGLKMGDKTLTV 368
           N  +   + + V
Sbjct: 61  NESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.7 bits (95), Expect = 8e-05
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG +P   TE +++ + E  G +    ++KD+ TG+ +G  F  Y      D A  A
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 356 LNG---LKMGDKTLTVRRA 371
           L+    L  G   + VR A
Sbjct: 61  LHNQRTLPGGASPVQVRYA 79

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    +++ ++     +G L    ++ D +T  S+G+GF  +      D     
Sbjct: 4   KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEAD-EAME 62

Query: 356 LNGLKMGDKTLTVRRA 371
                +    + ++RA
Sbjct: 63  AQPHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

>gnl|CDD|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 40.3 bits (95), Expect = 8e-05
 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  LP+  T   +K+L    G +   D+  D D G SKG+G  +++ P     A    
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 357 NGLKMGDKTLTVR 369
           NG  +  + L VR
Sbjct: 60  NGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional

 Score = 42.3 bits (99), Expect = 8e-05
 Identities = 19/85 (22%), Positives = 42/85 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +   +  +++    FG +    ++ DR+TG S+G+GF  + D      A + 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
           ++G ++  + + V  A       + 
Sbjct: 96  MDGKELNGRHIRVNPANDRPSAPRA 120

Length = 144

>gnl|CDD|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 40.4 bits (94), Expect = 8e-05
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL    T   +K+  E FG +    L+ D+ T   +G+GF  ++   + +  C
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDI 351
           ++FVGGL    TE +I+E    FG +   +L  D+ T   +G+ F  +     V  I
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 40.3 bits (94), Expect = 9e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           V GL  Y TE  ++E+   +G L G ++V D+ TG S+G+ F  ++    +  A    NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 359 LKMGDKTLTV 368
           +++  + + V
Sbjct: 64  MELDGRRIRV 73

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 28/88 (31%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 31  RGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSD 90
           R R R  R  +  G  R RD+    +R   R   R +R R   R + R      RS S  
Sbjct: 3   RSRSRSPRRSRRRGRSRSRDRR---ERRRERSRSR-ERDRR-RRSRSRSPHRSRRSRS-- 55

Query: 91  RFRNRSKSLSPSRSPSKSKRRSGFDMAP 118
             R+RS+S SPSR   + + R      P
Sbjct: 56  PRRHRSRSRSPSRRRDRKRERDKDAREP 83

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)

 Score = 41.8 bits (98), Expect = 1e-04
 Identities = 28/71 (39%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 44  GDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRS---HSSDRFRNRSKSLS 100
           G  R R       R   R  DR +R R+ +R +ER  R RSRS   H S R R+  +  S
Sbjct: 2   GRSRSRSPRRSRRRGRSRSRDRRERRRERSRSRERDRRRRSRSRSPHRSRRSRSPRRHRS 61

Query: 101 PSRSPSKSKRR 111
            SRSPS+ + R
Sbjct: 62  RSRSPSRRRDR 72

This is a family of eukaryotic proteins of unknown function. Some of the proteins in this family are putative nucleic acid binding proteins. Length = 158

>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +FVGGL +  T+  +KE    FG +    +  D  TG S+G+GF +++D A  +
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVE 54

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 17/82 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRT 231
           VYV G P  A    I  FF +               V N+ +  + +KKF    FVE +T
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGK------------VNNIRMRRDLDKKFKGSVFVEFKT 49

Query: 232 VEEASNAMALDGIIFEGVAVRV 253
            E+A   +  + + ++   + V
Sbjct: 50  EEDAKKFLEKEKLKYKEKELTV 71

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA A 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+ + +  K L VR
Sbjct: 57  LDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 39.8 bits (94), Expect = 1e-04
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----FAFVEMRTV 232
           +YVG L     E+ I   FS+          G    ++ + ++   K    F FVE  T 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSR---------CGDIKRII-MGLDRFTKTPCGFCFVEYYTR 50

Query: 233 EEASNAMA-LDGIIFEGVAVRV 253
           E+A NA+  L+G   +   +RV
Sbjct: 51  EDAENAVKYLNGTKLDDRIIRV 72

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 20/60 (33%), Positives = 34/60 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E  E +GTL    +++D  T  S+G+GF  Y      D A +A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++F+GGL +  +   +++    FG +    +++D  T  S+G+GF  + DPA  D
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVD 55

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 19/84 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE------KKFAFVEMR 230
           V+VG +P  A E+ +   FS+V         GP   VV+  +  +      K + F E  
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEV---------GP---VVSFRLVTDRDTGKPKGYGFCEFE 48

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
            +E A++A+  L+G  F G A+RV
Sbjct: 49  DIETAASAIRNLNGYEFNGRALRV 72

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

>gnl|CDD|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 13/50 (26%), Positives = 28/50 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 51

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +P    E ++  L E  G ++   L+ D   G ++GY F  Y +      A   L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 357 NGLKM-GDKTLTV 368
           +  ++   K L V
Sbjct: 63  HNYEIRPGKRLGV 75

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 27/55 (49%)

Query: 306 FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK 360
            T+ Q+  L +    L   DL +D  TG SKG+ +  Y +PA    A   LNG +
Sbjct: 11  VTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKLNGFE 65

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +FVG L    T+  ++E   + + ++ G  +V D  TG SKGYGF  + D    D A   
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 356 LNGLKMGDKTLTVRRAT 372
           +NG+    + + V  AT
Sbjct: 64  MNGVYCSSRPMRVSPAT 80

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 38/80 (47%), Gaps = 14/80 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           +VYVG L P A ++ +   F +          GP   + +V++      FAFVE     +
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKY---------GP---LRSVWVARNPPGFAFVEFEDPRD 48

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+ ALDG    G  VRV
Sbjct: 49  AEDAVRALDGRRICGNRVRV 68

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 39.5 bits (93), Expect = 2e-04
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTDIAC 353
           ++V  L +   E  ++ +   FG +    + K +D    +   G+ F  ++D +      
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDAS------ 56

Query: 354 AALNGLKMGDKTLTVRRATAS 374
           +A N L++    L  R+ + S
Sbjct: 57  SAENALQLNGTELGGRKISVS 77

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 13/46 (28%), Positives = 28/46 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           ++FVG +P  ++E  ++EL E +G ++  ++++DR     +  G C
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCC 48

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 16/63 (25%), Positives = 28/63 (44%)

Query: 299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG 358
           +G L  +  E  I       G +    +++++ TG S GYGF  +      + A  +LNG
Sbjct: 4   MGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNG 63

Query: 359 LKM 361
             +
Sbjct: 64  KPI 66

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

>gnl|CDD|241205 cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 19/60 (31%), Positives = 33/60 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D A  A
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIA 352
           R+++G L    TE  + +L   +G +  FD +  +     G  +GY F  ++     + A
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 353 CAALNGLKMGDKTLTVRRA 371
             +LNG     K L VR A
Sbjct: 61  LKSLNGKTALGKKLVVRWA 79

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.5 bits (100), Expect = 3e-04
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 1/74 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L        + +    FG +    +  D + G S+GYGF  ++       A   +
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 357 NGLKMGDKTLTVRR 370
           NG+ + DK + V R
Sbjct: 150 NGMLLNDKEVYVGR 163

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           F+GGL +  T   ++E    FG +    +++D  T  S+G+GF  + DPA  D
Sbjct: 2   FIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVD 54

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|240846 cd12400, RRM_Nop6, RNA recognition motif in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 17/56 (30%), Positives = 24/56 (42%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           +FVG LPY  T   +    ++ G      L+ D+ TG SKG  F  +        A
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA 58

This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. . Length = 74

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  ++  + E L  FG +    +  D  TG S+G+GF +++D A  D     
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVD-KVLE 59

Query: 356 LNGLKMGDKTLTVRRA 371
           L   K+  K +  +RA
Sbjct: 60  LKEHKLDGKLIDPKRA 75

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE + K+L   +G      + K       KG+GF   +  A+ +IA A 
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFINK------GKGFGFIKLESRALAEIAKAE 56

Query: 356 LNGLKMGDKTLTVR 369
           L+   M  + L VR
Sbjct: 57  LDDTPMRGRQLRVR 70

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 15/79 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VG LP     + +   F +  T          D V        K + FV M   E+A
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVT------ECDVV--------KNYGFVHMEEEEDA 46

Query: 236 SNAM-ALDGIIFEGVAVRV 253
            +A+ AL+G  F G  + V
Sbjct: 47  EDAIKALNGYEFMGKRINV 65

This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. . Length = 66

>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 18/73 (24%), Positives = 37/73 (50%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + VG L     +  +KE+  ++GT+   DL  DR+    +GY +  ++ P   + A   +
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 357 NGLKMGDKTLTVR 369
           +G ++  + +TV 
Sbjct: 61  DGGQIDGQEVTVE 73

This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. . Length = 73

>gnl|CDD|241118 cd12674, RRM1_Nop4p, RNA recognition motif 1 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 19/77 (24%), Positives = 32/77 (41%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  L +  T+  + +       +    +V D +TG S+GYGF  +        A A L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 357 NGLKMGDKTLTVRRATA 373
              K+  + L +  A  
Sbjct: 62  KNKKLHGRILRLDIAER 78

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 14/50 (28%), Positives = 29/50 (58%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+GF  + D
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDD 51

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 21/89 (23%)

Query: 173 HARRVYVGGLPP-LANEQAIATFFSQVMT------AIGGNSAGPGDAVVNVYINHEKKFA 225
           H+R ++V  LP    +   +   FSQV        AI   +  P              FA
Sbjct: 1   HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRG------------FA 47

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           FVE  T E+A  A  AL+G   +G  +RV
Sbjct: 48  FVEYATAEDAEEAQQALNGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 38.5 bits (90), Expect = 4e-04
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FVG L +   E  I E    +G +    L  D D+G  KG+G   Y + +  + A AAL
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFG---YVEFSSQEAAQAAL 57

Query: 357 NGL 359
           + L
Sbjct: 58  DAL 60

This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. . Length = 73

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 296 RVFVGGLPYYFTETQIKELL-ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+  +PY      +K+L  E  G +   +L KD + G S+G G   ++D      A  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 355 ALNGLKMGDKTLTVR 369
            +N  ++  + L V+
Sbjct: 60  TMNRYELKGRKLVVK 74

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L    T+ ++++  E +G L    + +     N  G+ F  ++DP   + A  A
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 356 LNGLKMGDKTLTV 368
           L+G ++    + V
Sbjct: 56  LDGRRICGNRVRV 68

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

>gnl|CDD|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 10/94 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  L     E +++EL   FG +    ++KD  +G S+G+ F  ++       A   +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 357 NGLKMGD----KTLTVRRATASSGQSKTEQESIL 386
           NG K+G     K L V RA     Q + E+E+ L
Sbjct: 240 NGKKIGLAKEGKKLYVGRA-----QKRAEREAEL 268

These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis (GP:11610605_PABP3 ), platelets (SP:Q13310_PABP4 ), broadly expressed (SP:P11940_PABP1) and of unknown tissue range (SP:Q15097_PABP2). Length = 562

>gnl|CDD|240885 cd12439, RRM_TRMT2A, RNA recognition motif in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 5/79 (6%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +V +  LP Y    Q+K+ L+       F   K +     + + F  ++       A  
Sbjct: 6   FKVEIKNLPKYIGFKQLKKFLKK----QLFKPHKIKLLKR-QDFAFVTFRSEEERQKALE 60

Query: 355 ALNGLKMGDKTLTVRRATA 373
            L+G K   + L+ R A  
Sbjct: 61  ILDGFKWKGRVLSARLAKP 79

This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. . Length = 79

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 38.3 bits (89), Expect = 5e-04
 Identities = 18/62 (29%), Positives = 35/62 (56%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  LP   TE +++++ E++G +   +L++D+ TG  +G  F  Y        A ++L
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 357 NG 358
           NG
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241096 cd12652, RRM2_Hu, RNA recognition motif 2 in the Hu proteins family

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V GLP   T+ +++ L   +G +    ++ D  TG S+G GF  +      + A  AL
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 357 NGLKMGDKT--LTVRRA 371
           NG      T  +TV+ A
Sbjct: 63  NGTIPPGATEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 41.5 bits (97), Expect = 6e-04
 Identities = 32/110 (29%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +S +I GA     ++V GLP   T+ +++ +   FG +    ++ D  TG SKG GF  +
Sbjct: 83  SSDSIKGAN----LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF 138

Query: 344 QDPAVTDIACAALNGLKMGDKT--LTVRRATASSGQSKTEQESILAQAQQ 391
                 D A   LNG      T  +TV+ A   S  +     S L   Q 
Sbjct: 139 DKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQN 188

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins

 Score = 37.9 bits (89), Expect = 6e-04
 Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 12/78 (15%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVK------DRDTGNSKGYGFCVYQDPAVTD 350
           ++VG L +Y TE QI EL    G       +K      DR T    G+ F  Y      +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGD------IKRIIMGLDRFTKTPCGFCFVEYYTREDAE 54

Query: 351 IACAALNGLKMGDKTLTV 368
            A   LNG K+ D+ + V
Sbjct: 55  NAVKYLNGTKLDDRIIRV 72

This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. . Length = 78

>gnl|CDD|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V GLP   T+ ++++L   +G +    +++D+ TG S+G GF  +      + A   L
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 357 NGLKM--GDKTLTVRRA 371
           NG K     + +TV+ A
Sbjct: 63  NGQKPEGASEPITVKFA 79

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 38.2 bits (88), Expect = 7e-04
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +      D A AA
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.3 bits (88), Expect = 7e-04
 Identities = 18/60 (30%), Positives = 31/60 (51%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GLP   T+  + +L + +G +     + D+ T   KGYGF  +  PA    A +AL
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAVSAL 69

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term

 Score = 37.5 bits (87), Expect = 0.001
 Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 4  RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           +IR  A  +  R + S      R   R +    R  +    DR R ++        RD 
Sbjct: 23 EEIRRKAERDVDRGRRSPRRRTRRRSRRRKRSRKRRRRRRDRDRARYRDRDDRD---RDR 79

Query: 64 DRTDRHRDYNRDKERRHR 81
              R R  +R ++RR R
Sbjct: 80 YDRSRSRSRSRSRDRRRR 97

This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. Length = 97

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 15/81 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV--EMRTVE 233
           R++VG LPP   E+ +   F +   A              ++I+ +K F F+  E RT+ 
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKA------------GEIFIHKDKGFGFIRLETRTLA 50

Query: 234 EASNAMALDGIIFEGVAVRVR 254
           E + A  LD +   G  +RVR
Sbjct: 51  EIAKA-ELDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 56

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FV  LP+  T  ++KE     G +  F  +K  + G SKG G   +  P   + AC  
Sbjct: 1   QIFVRNLPFDLTWQKLKEKFSQCGHVM-FAEIK-MENGKSKGCGTVRFDSPESAEKACRL 58

Query: 356 LNGLKMGDKTLTVR 369
           +NG+K+  + + VR
Sbjct: 59  MNGIKINGREIDVR 72

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.2 bits (86), Expect = 0.001
 Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 8/73 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG LP   TE +I+ L E +G +   D++K+        YGF    D    D A   
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53

Query: 356 LNGLKMGDKTLTV 368
           L+  K+    + V
Sbjct: 54  LHHYKLHGVAINV 66

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 37.1 bits (86), Expect = 0.001
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           ++FVGGL +  T+  ++     +G +    ++KD+ T  S+G+GF  ++DP
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP 51

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 16/81 (19%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           +YVG L     E  +A  FSQ+         GP   + +  +  E     +AFVE     
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQI---------GP---IKSCKLIREHGNDPYAFVEYYDHR 48

Query: 234 EASNA-MALDGIIFEGVAVRV 253
            A+ A   ++G +  G  ++V
Sbjct: 49  SAAAALQTMNGRLILGQEIKV 69

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           ++FVGGL    TE +I+E    FG +   +L  D  T   +G+ F  +++
Sbjct: 6   KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKE 55

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

>gnl|CDD|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 17/58 (29%), Positives = 30/58 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           ++FVGGL        +K+  E FG +    L+ D+ T   +G+GF  +++  V +  C
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVC 62

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +++G L  Y  E  IK    S G T+    +++++ TG   GY F  + D A  +     
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 356 LNGL 359
           LNG 
Sbjct: 62  LNGK 65

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

>gnl|CDD|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 19/84 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           ++V  LPP A+E  +   F             P  AV NV +      N  K + FV M 
Sbjct: 4   IFVYNLPPDADESLLWQLF------------SPFGAVTNVKVIRDLTTNKCKGYGFVTMT 51

Query: 231 TVEEASNAMA-LDGIIFEGVAVRV 253
             EEA +A+A L+G    G  ++V
Sbjct: 52  NYEEAYSAIASLNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 15/80 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV------NVYINHEKKFAFVE 228
           R +YV  L    +E  +   FS+          G  +++                FAFV 
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSK---------FGEVESIRIPKKQDEKQGRLNNGFAFVT 51

Query: 229 MRTVEEASNAMALDGIIFEG 248
            +    A NA+ L+G    G
Sbjct: 52  FKDASSAENALQLNGTELGG 71

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 37.1 bits (85), Expect = 0.002
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GLP   T+  + +L + +G +     + D++T   KGYGF  +  PA    A A+L
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAVASL 66

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 22/58 (37%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTL-----HGFD---LVKDRDTGNSKGYGFCVYQDP 346
           VFV  LP   TE  + E   S G +      G     L KD+DTG  KG     Y DP
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDP 58

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVG L    TE +++E+   +G +    +++D +   S+G  F  Y    +   A  A
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRD-EMKQSRGCAFVKYSSKEMAQAAIKA 59

Query: 356 LNGL---KMGDKTLTVRRA 371
           LNG+   +  D+ L VR A
Sbjct: 60  LNGVYTMRGCDQPLIVRFA 78

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEMR 230
           ++V GL     E+ +   FS+          G    V  V +  + +      F FV   
Sbjct: 4   LFVSGLSTRTTEKELEALFSKF---------GR---VEEVLLMKDPETGESRGFGFVTFE 51

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR 255
           +VE+A  A+  L+G   EG  ++V +
Sbjct: 52  SVEDADAAIRDLNGKELEGRVIKVEK 77

This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. . Length = 80

>gnl|CDD|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
            V++G L +  TE  ++E  +    +    L  D++TG  KG+G   + D    D A
Sbjct: 1   TVYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAA 56

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

>gnl|CDD|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV++G L Y+  E  I+     +G L   DL          GYGF  ++D    D A   
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEIDL--------KNGYGFVEFEDSRDADDAVYE 52

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG  +  + + V  A
Sbjct: 53  LNGKDLCGERVIVEHA 68

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG L    T+  +      + +     +V+D+ TG SKGYGF  + DP   D   A 
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN--DYLKAM 65

Query: 356 --LNGLKMGDKTLTVRRA 371
             +NG  +G++ + +R++
Sbjct: 66  KEMNGKYVGNRPIKLRKS 83

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

>gnl|CDD|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 17/54 (31%), Positives = 30/54 (55%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +F+GGL +  T+  +K+    FG +    L  D  TG S+G+GF ++++    D
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD 54

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 5/76 (6%)

Query: 297 VFVGGLPYYFTETQIK-ELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           +FV G      E  I+  L E F   G +    +  DR+TG SKG+ +  ++     + A
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 353 CAALNGLKMGDKTLTV 368
              L+G  +G   L V
Sbjct: 62  -LELDGSDLGGGNLVV 76

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 19/61 (31%), Positives = 30/61 (49%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+V  LP   T   +K +   +GT+    L + + TG+ KG+ F  ++ P     AC  L
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 357 N 357
           N
Sbjct: 62  N 62

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+F+       TE  ++E    FG +    +VKD+ T  SKG  +  +   A    A  A
Sbjct: 5   RLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF---AKASSAARA 60

Query: 356 ---LNGLKMGDKTLTVR 369
              +NG  +G  T  ++
Sbjct: 61  MEEMNGKCLGGDTKPLK 77

This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

>gnl|CDD|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           VFV  L Y   E ++++L    G +    LVK+   G SKGY +  +++
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFEN 49

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 12/80 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R + +  +    NE+ I  FF +    IG +       V  + +  + + A VE  +  +
Sbjct: 1   RTIGLFNVSDTVNEEQIKAFFEK----IGPD-------VRKIELFPDHEGALVEFESPSD 49

Query: 235 ASNA-MALDGIIFEGVAVRV 253
           A  A ++L+G  F G  +++
Sbjct: 50  AGKASLSLNGSQFGGKTIKI 69

This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 71

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	435
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.98
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.93
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.92
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.9
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.87
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.87
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.86
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.85
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.85
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.85
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.84
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.84
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.84
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.82
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.79
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.79
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.74
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.72
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.7
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.68
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.66
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.66
KOG0122	270	consensus Translation initiation factor 3, subunit	99.65
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.65
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.63
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.62
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.61
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.61
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.61
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.6
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.59
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.59
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.58
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.58
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.57
PLN03120	260	nucleic acid binding protein; Provisional	99.55
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.54
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.53
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.52
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.51
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.5
PLN03213	759	repressor of silencing 3; Provisional	99.5
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.49
smart00362	72	RRM_2 RNA recognition motif.	99.48
smart00360	71	RRM RNA recognition motif.	99.46
PLN03121	243	nucleic acid binding protein; Provisional	99.46
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.46
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.44
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.44
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.44
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.43
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.43
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.42
PLN03120	260	nucleic acid binding protein; Provisional	99.42
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.4
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.4
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.39
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.39
smart00361	70	RRM_1 RNA recognition motif.	99.38
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.36
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.35
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.35
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.34
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.33
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.32
PLN03121	243	nucleic acid binding protein; Provisional	99.31
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.31
KOG0122	270	consensus Translation initiation factor 3, subunit	99.3
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.27
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.27
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	99.27
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.25
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.25
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.23
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.22
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.19
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.17
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.17
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.15
smart00362	72	RRM_2 RNA recognition motif.	99.15
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.15
PLN03213	759	repressor of silencing 3; Provisional	99.14
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.14
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.13
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.09
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.07
KOG4210	285	consensus Nuclear localization sequence binding pr	99.06
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.05
KOG0226	290	consensus RNA-binding proteins [General function p	99.04
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	99.02
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.99
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.99
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.99
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.94
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.94
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.93
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.93
smart00360	71	RRM RNA recognition motif.	98.9
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.88
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.85
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.84
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.83
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.78
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.78
smart00361	70	RRM_1 RNA recognition motif.	98.76
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.76
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.75
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.65
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.63
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.63
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.58
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.52
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.52
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.48
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.46
KOG0151	877	consensus Predicted splicing regulator, contains R	98.41
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.33
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.31
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.22
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.19
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.14
KOG0151	877	consensus Predicted splicing regulator, contains R	98.06
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.05
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.02
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.02
KOG0226	290	consensus RNA-binding proteins [General function p	97.99
PF06495	182	Transformer: Fruit fly transformer protein; InterP	97.97
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.96
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.95
KOG2314	698	consensus Translation initiation factor 3, subunit	97.91
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.82
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.72
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.71
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.69
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.66
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.64
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.62
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.48
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.41
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.4
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.34
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.31
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.15
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	97.1
KOG3152	278	consensus TBP-binding protein, activator of basal	97.08
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.93
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.87
KOG2135	526	consensus Proteins containing the RNA recognition	96.84
KOG2135	526	consensus Proteins containing the RNA recognition	96.81
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.78
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.68
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.64
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.39
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.28
KOG3152	278	consensus TBP-binding protein, activator of basal	95.98
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	95.93
KOG4210	285	consensus Nuclear localization sequence binding pr	95.88
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	95.87
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.85
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	95.8
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	95.73
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	95.68
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.59
KOG2548	653	consensus SWAP mRNA splicing regulator [RNA proces	95.56
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.42
KOG2314	698	consensus Translation initiation factor 3, subunit	95.31
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.28
KOG3263	196	consensus Nucleic acid binding protein [General fu	95.21
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.12
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.09
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	94.74
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.3
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	94.16
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	93.3
KOG1996	378	consensus mRNA splicing factor [RNA processing and	92.8
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	92.69
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.38
KOG2891	445	consensus Surface glycoprotein [General function p	92.34
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	91.59
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	90.24
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	89.64
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	88.56
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.27
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	87.56
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	87.39
KOG2318	650	consensus Uncharacterized conserved protein [Funct	87.2
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	84.65
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	84.48
KOG1882	293	consensus Transcriptional regulator SNIP1, contain	84.07
KOG2591	684	consensus c-Mpl binding protein, contains La domai	83.73
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	82.89
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	81.61

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=1.7e-45  Score=372.70  Aligned_cols=256  Identities=44%  Similarity=0.686  Sum_probs=191.7

Q ss_pred             ccchhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCc
Q 013837          165 VMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI  244 (435)
Q Consensus       165 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~  244 (435)
                      .+..+.....++|||+|||+.+|+++|.+||..++..++.....++..|..+.++.++|||||+|.+.++|..||+|+|+
T Consensus       166 ~~~~~~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       166 PYQQQATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             ccCccCCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            34567788899999999999999999999999998887766555567889999999999999999999999999999999


Q ss_pred             eecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 013837          245 IFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v  324 (435)
                      .|.|++|+|.++..+.+............+.....................+|||+|||..+|+++|+++|+.||.|..+
T Consensus       246 ~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       246 IYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF  325 (509)
T ss_pred             EeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE
Confidence            99999999998887764332222222222221111111111122233556899999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccC
Q 013837          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSG  404 (435)
Q Consensus       325 ~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  404 (435)
                      .|+++..+|.++|||||+|.+.++|..||..|||..|+|+.|.|.+|...............      ...   ......
T Consensus       326 ~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~------~~~---~~~~~~  396 (509)
T TIGR01642       326 NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGM------APV---TLLAKA  396 (509)
T ss_pred             EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccc------ccc---cccccc
Confidence            99999889999999999999999999999999999999999999999765433322111100      000   000000


Q ss_pred             CcccCCCCCCCCCCcceeEEeccccccC
Q 013837          405 MNTLGGGMSLFGETLAKVLCLTEMMKSM  432 (435)
Q Consensus       405 ~~~~~~~~~~~~~~p~~v~~l~n~~~~~  432 (435)
                         ....+...+..|+.||+|.||+++.
T Consensus       397 ---~~~~~~~~~~~~s~v~~l~N~~~~~  421 (509)
T TIGR01642       397 ---LSQSILQIGGKPTKVVQLTNLVTGD  421 (509)
T ss_pred             ---chhhhccccCCCceEEEeccCCchh
Confidence               0011112345689999999999763

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=100.00  E-value=4.1e-39  Score=321.68  Aligned_cols=181  Identities=28%  Similarity=0.436  Sum_probs=149.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .+...++|||+|||..+++++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+||.|+|..|.|+
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~------i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~  158 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQ------CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGR  158 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCe
Confidence            345678999999999999999999999999864421      23333456789999999999999999999999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      +|.|.++............              .   .........+|||+|||..+|+++|+++|+.||.|..|.|+.+
T Consensus       159 ~i~v~~~~~~~~~~~~~~~--------------~---~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d  221 (457)
T TIGR01622       159 PIIVQSSQAEKNRAAKAAT--------------H---QPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRD  221 (457)
T ss_pred             eeEEeecchhhhhhhhccc--------------c---cCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEc
Confidence            9999875432211110000              0   0001122679999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      +.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+..
T Consensus       222 ~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       222 PETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             CCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccC
Confidence            98899999999999999999999999999999999999999864

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=100.00  E-value=1.3e-32  Score=278.58  Aligned_cols=194  Identities=20%  Similarity=0.201  Sum_probs=142.4

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||..+|+++|.++|..||.|..+.      ++.+..++.++|||||+|.+.++|..|+ .|||+.|.|+.|
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~------~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l  367 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFN------LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKL  367 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            457999999999999999999999999875532      2334446778999999999999999999 699999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCC----------CHHHHHHHHHhcCCe
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYF----------TETQIKELLESFGTL  321 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~----------te~~l~~~F~~~G~v  321 (435)
                      .|.++................ +..................++.+|+|.||...-          ..++|+++|++||.|
T Consensus       368 ~v~~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v  446 (509)
T TIGR01642       368 HVQRACVGANQATIDTSNGMA-PVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPL  446 (509)
T ss_pred             EEEECccCCCCCCcccccccc-ccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCe
Confidence            999876433221110000000 000000000000011123456789999996421          236899999999999


Q ss_pred             eEEEEeecC---CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          322 HGFDLVKDR---DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       322 ~~v~i~~~~---~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      +.|.|+++.   .++...|+|||+|.++++|.+||.+|||.+|+|+.|.|.|...
T Consensus       447 ~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       447 INIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             eEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            999998752   3456789999999999999999999999999999999999843

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=3.1e-32  Score=256.59  Aligned_cols=171  Identities=19%  Similarity=0.310  Sum_probs=148.7

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||+++|+++|+++|..||.|+.+.      ++.+..++.++|||||+|.+.++|..|| +|++..|.+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~------i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~g  176 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCR------IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRN  176 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCC
Confidence            345678999999999999999999999999875532      2344456778999999999999999999 699999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~  328 (435)
                      ++|+|.++.+...                             ....++|||+|||..+|+++|+++|++||.|+.|.|+.
T Consensus       177 r~i~V~~a~p~~~-----------------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~  227 (346)
T TIGR01659       177 KRLKVSYARPGGE-----------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILR  227 (346)
T ss_pred             ceeeeeccccccc-----------------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEee
Confidence            9999998653210                             11235799999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q 013837          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASS  375 (435)
Q Consensus       329 ~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a~~~~  375 (435)
                      ++.+++++|||||+|.+.++|++||+.||+..|.|  +.|+|.+|+...
T Consensus       228 d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~  276 (346)
T TIGR01659       228 DKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHG  276 (346)
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCccc
Confidence            99899999999999999999999999999998865  799999997653

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.98  E-value=1.9e-32  Score=257.15  Aligned_cols=186  Identities=26%  Similarity=0.378  Sum_probs=151.7

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      ..+...++||+..|+..+++.+|.+||..+|.|..      +..|.+-....++|.|||+|.+.+....|+.|.|+.+.|
T Consensus       174 ~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrd------VriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg  247 (549)
T KOG0147|consen  174 PEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRD------VRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLG  247 (549)
T ss_pred             chHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcce------eEeeccccchhhcceeEEEEecccchhhHhhhcCCcccC
Confidence            35678899999999999999999999999998754      223455556778999999999999999999999999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~  328 (435)
                      .+|.|+.........+ ...+.              .+......+...|||+||.+++|+++|+.+|++||.|+.|.+.+
T Consensus       248 ~pv~vq~sEaeknr~a-~~s~a--------------~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~  312 (549)
T KOG0147|consen  248 VPVIVQLSEAEKNRAA-NASPA--------------LQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTK  312 (549)
T ss_pred             ceeEecccHHHHHHHH-hcccc--------------ccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeecc
Confidence            9999986543222111 00000              00001112222399999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       329 ~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      |.+||.++||+||+|.+.++|.+|++.|||+.|.|+.|+|...+...
T Consensus       313 d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~  359 (549)
T KOG0147|consen  313 DSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERV  359 (549)
T ss_pred             ccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeec
Confidence            98899999999999999999999999999999999999999886654

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.97  E-value=1.2e-31  Score=255.54  Aligned_cols=298  Identities=43%  Similarity=0.715  Sum_probs=230.0

Q ss_pred             CCCCCCCCCCccCCCccCCCCccCCCCCC--------CCCCCCCCCCCCCCccccccCCCCCCCCCCCCCCcccccchhh
Q 013837           99 LSPSRSPSKSKRRSGFDMAPPAAAMLPGA--------AVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQA  170 (435)
Q Consensus        99 rs~sr~~~~~~r~~~~~~~p~~~~~~~~~--------~~~g~~p~~~~~~p~~~~~~~~~~~~~~~~~~~~p~~~~~~~~  170 (435)
                      +.+++.+...+....|+.++++++..++.        ...|+.|+....+.....            .+..|++.+..++
T Consensus       104 ~r~~~~~~~~r~~~~~~~~~~~fe~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~~~~~  171 (500)
T KOG0120|consen  104 RRRSRSRRYSRKRSLWDVPPEGFETITPDGAKLYKNFNATGQVPGDLSNPKKSLK------------LPQLPTPPMDSQA  171 (500)
T ss_pred             cccccccccccchhhhcCCCCCCcccCchhhhhhhhccccCCCCCCccccccccc------------cccCCCCccCcch
Confidence            34445555577788899999999998874        233333333221111100            3344555666778


Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ...+..++|+++|+.++++....+|..--.+.+++....+..++.+.++..++||||+|.+.++|..|+.+++..+.|.+
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~  251 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKNFAFIEFRSISEATEAMALDGIIFEGRP  251 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccccceeEEecCCCchhhhhcccchhhCCCC
Confidence            88899999999999999999999999987777777776678899999999999999999999999999999999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                      +++..+..+.+.........+      ....+............+.+||++||..+++..+.++...||.+....++++.
T Consensus       252 ~~~~r~~d~~~~p~~~~~~~~------~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~  325 (500)
T KOG0120|consen  252 LKIRRPHDYQPVPGITLSPSQ------LGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS  325 (500)
T ss_pred             ceecccccccCCccchhhhcc------ccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence            999998888766554444333      22223334455566777899999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCchHHHHHHHHHHHHHHHHHHHhhccCCcccCC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGG  410 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  410 (435)
                      .+|.++||||.+|.+...+..|+..|||..++++.|.|+.|............    ..              +..+++.
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~----~~--------------~~~~~~i  387 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFN----IS--------------QSQVPGI  387 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCC----cc--------------ccccccc
Confidence            99999999999999999999999999999999999999999776543332111    00              0011222


Q ss_pred             CCC--CCCCCcceeEEeccccccC
Q 013837          411 GMS--LFGETLAKVLCLTEMMKSM  432 (435)
Q Consensus       411 ~~~--~~~~~p~~v~~l~n~~~~~  432 (435)
                      ...  .+...|+.||+|+|||+|.
T Consensus       388 ~~~~~q~~g~~t~Vl~L~n~Vt~d  411 (500)
T KOG0120|consen  388 PLLMTQMAGIPTEVLCLTNVVTPD  411 (500)
T ss_pred             hhhhcccCCCcchhhhhhhcCCHH
Confidence            221  3445899999999999984

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.97  E-value=6.8e-31  Score=259.70  Aligned_cols=182  Identities=26%  Similarity=0.392  Sum_probs=151.7

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      +....++|||+|||+.+++++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|..|+ .|||..|.|
T Consensus       103 a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~------I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~G  176 (612)
T TIGR01645       103 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSIN------MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG  176 (612)
T ss_pred             hhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEE------EeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEec
Confidence            346778999999999999999999999999875532      2334456788999999999999999999 699999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~  328 (435)
                      +.|+|.++.......        +.  ..        ..........+|||+|||..+++++|+++|+.||.|+.+.|++
T Consensus       177 R~IkV~rp~~~p~a~--------~~--~~--------~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~  238 (612)
T TIGR01645       177 RNIKVGRPSNMPQAQ--------PI--ID--------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  238 (612)
T ss_pred             ceeeecccccccccc--------cc--cc--------cccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEe
Confidence            999998754332100        00  00        0001122346899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       329 ~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++.+|.++|||||+|.+.++|.+||+.|||+.|+|+.|+|.++..++
T Consensus       239 D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       239 APTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             cCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            99899999999999999999999999999999999999999998644

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.97  E-value=1.7e-29  Score=252.36  Aligned_cols=189  Identities=21%  Similarity=0.238  Sum_probs=136.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      .++|||+|||..+|+++|.++|..||.|..+.      ++.+..++.++|||||+|.+.++|..|+ .|||..|.|++|.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~------~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~  259 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQ------LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIK  259 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEE------EEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEE
Confidence            68999999999999999999999999864421      1222223467899999999999999999 6999999999999


Q ss_pred             EcCCCCCCcchhhc--CCC--------------------------------CCCCCCc------cccccccc--------
Q 013837          253 VRRPTDYNPTLAAA--LGP--------------------------------GQPSPNL------NLAAVGLA--------  284 (435)
Q Consensus       253 v~~~~~~~~~~~~~--~~~--------------------------------~~~~~~~------~~~~~~~~--------  284 (435)
                      |.++.+........  ...                                ..+....      .....+..        
T Consensus       260 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  339 (457)
T TIGR01622       260 VGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRY  339 (457)
T ss_pred             EEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccc
Confidence            99976432111000  000                                0000000      00000000        


Q ss_pred             ---------cC----CCCCCCCCCeEEEcCCCCCCC----------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEE
Q 013837          285 ---------SG----AIGGAEGPDRVFVGGLPYYFT----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC  341 (435)
Q Consensus       285 ---------~~----~~~~~~~~~~l~V~nLp~~~t----------e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV  341 (435)
                               ..    .........+|+|.||....+          .+||+++|++||.|+.|.|...    ...|++||
T Consensus       340 ~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV  415 (457)
T TIGR01622       340 ATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYL  415 (457)
T ss_pred             cccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEE
Confidence                     00    000224567899999955544          3689999999999999988643    35799999


Q ss_pred             EEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          342 VYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       342 ~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +|.++++|.+|++.|||.+|+|+.|.|.|..
T Consensus       416 ~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~  446 (457)
T TIGR01622       416 KFSSVDAALAAFQALNGRYFGGKMITAAFVV  446 (457)
T ss_pred             EECCHHHHHHHHHHhcCcccCCeEEEEEEEc
Confidence            9999999999999999999999999999984

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=3.3e-29  Score=242.03  Aligned_cols=197  Identities=23%  Similarity=0.374  Sum_probs=145.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      ..++|||+|||..+++++|.++|..||.|+.+.      ++.+...+.++|||||+|.+.++|..|+ .|||..+.|  .
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~------~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~  161 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSR------ILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTE  161 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEE------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCce
Confidence            456899999999999999999999999864321      1112224567899999999999999999 699999887  5


Q ss_pred             eEEEcCCCCCCcchhhcCC--------CCCCC-------------------------CCccc------------------
Q 013837          250 AVRVRRPTDYNPTLAAALG--------PGQPS-------------------------PNLNL------------------  278 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~--------~~~~~-------------------------~~~~~------------------  278 (435)
                      +|.|.++............        +....                         .....                  
T Consensus       162 ~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (352)
T TIGR01661       162 PITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAA  241 (352)
T ss_pred             eEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhccccccccc
Confidence            6888876533211000000        00000                         00000                  


Q ss_pred             ----------cccccccC--CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCH
Q 013837          279 ----------AAVGLASG--AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP  346 (435)
Q Consensus       279 ----------~~~~~~~~--~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~  346 (435)
                                .......+  .........+|||+|||+.+++++|.++|++||.|..|.|+.+..||.++|||||+|.+.
T Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~  321 (352)
T TIGR01661       242 QRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNY  321 (352)
T ss_pred             ccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCH
Confidence                      00000000  000112334799999999999999999999999999999999998999999999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          347 AVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       347 ~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++|.+||..|||..|+|+.|+|.|+..+.
T Consensus       322 ~~A~~Ai~~lnG~~~~gr~i~V~~~~~~~  350 (352)
T TIGR01661       322 DEAAMAILSLNGYTLGNRVLQVSFKTNKA  350 (352)
T ss_pred             HHHHHHHHHhCCCEECCeEEEEEEccCCC
Confidence            99999999999999999999999997764

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=4.4e-29  Score=214.12  Aligned_cols=182  Identities=18%  Similarity=0.331  Sum_probs=152.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      .--|||+.|...++.++|++.|.+||+|..+      .+|.+..++++|||+||.|.+.++|+.|| +|||+=|+++.|.
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~a------kvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDA------KVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccc------eEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            4569999999999999999999999999774      46899999999999999999999999999 6999999999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      -.|+.-.....             +........--.......++|||+|++..+||++|++.|+.||.|.+|+|+++   
T Consensus       136 TNWATRKp~e~-------------n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~---  199 (321)
T KOG0148|consen  136 TNWATRKPSEM-------------NGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD---  199 (321)
T ss_pred             ccccccCcccc-------------CCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc---
Confidence            99987554110             00000000001112234578999999999999999999999999999999998   


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCch
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT  380 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~~~~  380 (435)
                         +|||||.|++.|.|.+||..+||..|.|..|++.|-+........
T Consensus       200 ---qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~~~  244 (321)
T KOG0148|consen  200 ---QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGINN  244 (321)
T ss_pred             ---cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCCCCc
Confidence               689999999999999999999999999999999999887654443

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=2e-28  Score=236.59  Aligned_cols=168  Identities=23%  Similarity=0.371  Sum_probs=144.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ...+|||+|||..+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|| .|||..|.|+.|
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~------i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i   75 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCK------LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI   75 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEE------EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeE
Confidence            356899999999999999999999999875532      1333345678999999999999999999 599999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~  331 (435)
                      .|.++.+...                             .....+|||+|||..+++++|.++|+.||.|..+.|+.+..
T Consensus        76 ~v~~a~~~~~-----------------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~  126 (352)
T TIGR01661        76 KVSYARPSSD-----------------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV  126 (352)
T ss_pred             EEEeeccccc-----------------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCC
Confidence            9998653211                             12245899999999999999999999999999999999888


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASS  375 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a~~~~  375 (435)
                      ++.++|||||+|.+.++|..||+.|||..+.|  ..|.|.|+....
T Consensus       127 ~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       127 TGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             CCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEECCCCC
Confidence            88999999999999999999999999999977  678999986543

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.96  E-value=3.1e-28  Score=221.60  Aligned_cols=174  Identities=25%  Similarity=0.397  Sum_probs=148.2

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCC-cee
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIF  246 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~-~~~  246 (435)
                      ..+.+.-+|||+-||..++|.||+.+|++||.|..++      ++.|..++.++|||||.|.+.++|.+|+ .|++ ++|
T Consensus        29 ~~d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~ein------l~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktl  102 (510)
T KOG0144|consen   29 NPDGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEIN------LIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTL  102 (510)
T ss_pred             CCCchhhhheeccCCccccHHHHHHHHHHhCceeEEE------eecccccCcccceEEEEeccHHHHHHHHHHhhccccc
Confidence            4456777899999999999999999999999987754      4777888999999999999999999999 5555 567


Q ss_pred             cC--ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 013837          247 EG--VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (435)
Q Consensus       247 ~g--~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v  324 (435)
                      -|  .+|.|+++......                            .....+|||+-|+..+||.+|+++|++||.|++|
T Consensus       103 pG~~~pvqvk~Ad~E~er----------------------------~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~  154 (510)
T KOG0144|consen  103 PGMHHPVQVKYADGERER----------------------------IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDC  154 (510)
T ss_pred             CCCCcceeecccchhhhc----------------------------cccchhhhhhhccccccHHHHHHHHHhhCccchh
Confidence            66  67888887543211                            1234689999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCC--eEEEEEEccCCCCC
Q 013837          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGD--KTLTVRRATASSGQ  377 (435)
Q Consensus       325 ~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~-~~~g--~~l~V~~a~~~~~~  377 (435)
                      .|++|.+ +.++|||||+|.+.+.|..||++|||. .+.|  .+|.|.||..++..
T Consensus       155 ~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk  209 (510)
T KOG0144|consen  155 YILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDK  209 (510)
T ss_pred             hheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCc
Confidence            9999964 999999999999999999999999986 4554  68999999877543

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.95  E-value=4.6e-28  Score=221.56  Aligned_cols=199  Identities=18%  Similarity=0.239  Sum_probs=148.4

Q ss_pred             cchhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       166 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      +........|.|||+.||.++.|++|.-+|+..|+|..+-      .+.+...+.++|||||.|++.++|++|+ .||++
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elR------LMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~  148 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELR------LMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNY  148 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEE------EeecccCCCCcceEEEEeecHHHHHHHHHHhhCc
Confidence            4445556789999999999999999999999999987642      3566678899999999999999999999 69999


Q ss_pred             ee-cCceEEEcCCCCCCcc----------------hhhcCCC--------CCCC-CCc----------------------
Q 013837          245 IF-EGVAVRVRRPTDYNPT----------------LAAALGP--------GQPS-PNL----------------------  276 (435)
Q Consensus       245 ~~-~g~~l~v~~~~~~~~~----------------~~~~~~~--------~~~~-~~~----------------------  276 (435)
                      +| .|+.|.|.-+......                .....++        ..+. ...                      
T Consensus       149 Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl  228 (506)
T KOG0117|consen  149 EIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKL  228 (506)
T ss_pred             cccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhc
Confidence            88 4777777643221110                0000000        0000 000                      


Q ss_pred             --------------cccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEE
Q 013837          277 --------------NLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV  342 (435)
Q Consensus       277 --------------~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~  342 (435)
                                    .|+.....+ ........+.|||+||+.++|||.|+++|+.||.|+.|+.++|        ||||.
T Consensus       229 ~~g~~klwgn~~tVdWAep~~e~-ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVH  299 (506)
T KOG0117|consen  229 MPGKIKLWGNAITVDWAEPEEEP-DEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVH  299 (506)
T ss_pred             cCCceeecCCcceeeccCcccCC-ChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEe
Confidence                          010000001 1112334567999999999999999999999999999998876        99999


Q ss_pred             EcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCc
Q 013837          343 YQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK  379 (435)
Q Consensus       343 f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~~~  379 (435)
                      |.+.++|.+||+.|||..|.|..|.|.+|++...+++
T Consensus       300 f~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  300 FAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             ecchHHHHHHHHHhcCceecCceEEEEecCChhhhcc
Confidence            9999999999999999999999999999988765444

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.94  E-value=1.1e-26  Score=237.39  Aligned_cols=165  Identities=19%  Similarity=0.360  Sum_probs=140.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      +|||+|||.++||++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .+++..|.|++|.|.
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~------v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~   75 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVR------VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIM   75 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEee
Confidence            699999999999999999999999864421      1223334678899999999999999999 699999999999999


Q ss_pred             CCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC
Q 013837          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (435)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~  334 (435)
                      |+.....                           .......+|||+|||.++++++|+++|+.||.|+.|.|+.+. +|+
T Consensus        76 ~s~~~~~---------------------------~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~  127 (562)
T TIGR01628        76 WSQRDPS---------------------------LRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGK  127 (562)
T ss_pred             ccccccc---------------------------ccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCC
Confidence            8643210                           001223579999999999999999999999999999999984 688


Q ss_pred             cceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       335 ~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ++|||||+|.+.++|.+|++.|||..+.|+.|.|.....+
T Consensus       128 skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~  167 (562)
T TIGR01628       128 SRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKK  167 (562)
T ss_pred             cccEEEEEECCHHHHHHHHHHhcccEecCceEEEeccccc
Confidence            9999999999999999999999999999999999876543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.94  E-value=1.9e-26  Score=228.09  Aligned_cols=190  Identities=19%  Similarity=0.261  Sum_probs=137.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec-C
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-G  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g  248 (435)
                      ....++|||+|||.+++|++|.++|..||.|+.+.      ++.+ ..+.++|||||+|.+.++|.+|| .||+..|. |
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vr------l~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~G  127 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELR------LMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPG  127 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEE------EEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCC
Confidence            34568999999999999999999999999876532      2333 56789999999999999999999 59998885 6


Q ss_pred             ceEEEcCCCCCCcc-------------hh---hcCCC---------C--CCCCCcccc--------------------c-
Q 013837          249 VAVRVRRPTDYNPT-------------LA---AALGP---------G--QPSPNLNLA--------------------A-  280 (435)
Q Consensus       249 ~~l~v~~~~~~~~~-------------~~---~~~~~---------~--~~~~~~~~~--------------------~-  280 (435)
                      +.|.|..+......             ..   .....         .  .........                    . 
T Consensus       128 r~l~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki  207 (578)
T TIGR01648       128 RLLGVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRI  207 (578)
T ss_pred             ccccccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccce
Confidence            76666544321100             00   00000         0  000000000                    0 


Q ss_pred             --------ccc-ccC---CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCcceEEEEEEcCH
Q 013837          281 --------VGL-ASG---AIGGAEGPDRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDP  346 (435)
Q Consensus       281 --------~~~-~~~---~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~v~~v~i~~~~~tg~~~G~afV~f~~~  346 (435)
                              +.. .+.   ........++|||+||+..+|+++|+++|+.|  |.|+.|.+++        +||||+|.+.
T Consensus       208 ~l~Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~  279 (578)
T TIGR01648       208 QLWGHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDR  279 (578)
T ss_pred             EecCceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCH
Confidence                    000 000   00112235689999999999999999999999  9999987754        4999999999


Q ss_pred             HHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          347 AVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       347 ~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++|.+||+.|||..|.|+.|+|.||++..
T Consensus       280 e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~  308 (578)
T TIGR01648       280 EDAVKAMDELNGKELEGSEIEVTLAKPVD  308 (578)
T ss_pred             HHHHHHHHHhCCCEECCEEEEEEEccCCC
Confidence            99999999999999999999999998764

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family

Probab=99.94  E-value=2.7e-26  Score=234.56  Aligned_cols=184  Identities=22%  Similarity=0.345  Sum_probs=146.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec---
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE---  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~---  247 (435)
                      ....+|||+|||..+|+++|+++|..||.|..+.       +.....+.++|||||+|.+.++|.+|+ .+++..|.   
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~-------i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~  248 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAA-------VMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAK  248 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEE-------EEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccc
Confidence            3456899999999999999999999999865421       222234567899999999999999999 69999999   


Q ss_pred             -CceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 013837          248 -GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (435)
Q Consensus       248 -g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i  326 (435)
                       |+.|.|.++................           ............+|||+||+..+|+++|+++|+.||.|.+|.|
T Consensus       249 ~g~~l~v~~a~~k~er~~~~~~~~~~-----------~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i  317 (562)
T TIGR01628       249 EGKKLYVGRAQKRAEREAELRRKFEE-----------LQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKV  317 (562)
T ss_pred             cceeeEeecccChhhhHHHHHhhHHh-----------hhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEE
Confidence             9999998876543221100000000           0000111234568999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      +.+ .+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+|..+
T Consensus       318 ~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       318 MLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             EEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            999 67999999999999999999999999999999999999999544

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.94  E-value=7.5e-26  Score=225.65  Aligned_cols=170  Identities=19%  Similarity=0.159  Sum_probs=138.3

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hCCceecCc
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEGV  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~~~~~~g~  249 (435)
                      ++++|||+|||+.+|+++|+++|..||.            |..+.+..+++||||+|.+.++|..|+.   +++..|.|+
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~------------V~~v~i~~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~   68 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGP------------VSYVMMLPGKRQALVEFEDEESAKACVNFATSVPIYIRGQ   68 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCC------------eeEEEEECCCCEEEEEeCchHHHHHHHHHhhcCCceEcCe
Confidence            3689999999999999999999999998            5555555688999999999999999994   588999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      +|.|.|+.........       ...          ..........+|+|.||++.+|+++|+++|+.||.|+.|.|+++
T Consensus        69 ~l~v~~s~~~~~~~~~-------~~~----------~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~  131 (481)
T TIGR01649        69 PAFFNYSTSQEIKRDG-------NSD----------FDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK  131 (481)
T ss_pred             EEEEEecCCcccccCC-------CCc----------ccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec
Confidence            9999998643211100       000          00011223357999999999999999999999999999999876


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEccCCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASS  375 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a~~~~  375 (435)
                      ..    .|+|||+|.+.++|.+|++.|||..|.|  +.|+|.|++...
T Consensus       132 ~~----~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       132 NN----VFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEYAKPTR  175 (481)
T ss_pred             CC----ceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEEecCCC
Confidence            42    4799999999999999999999999954  689999998644

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.94  E-value=7e-27  Score=189.44  Aligned_cols=170  Identities=25%  Similarity=0.407  Sum_probs=143.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~l  251 (435)
                      ...||||+||+..++++.|.++|-+.|.|+.+.+      -.+..+...+|||||||.+.++|.-|+. ||...|.|++|
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~i------PkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpI   81 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHI------PKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPI   81 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeec------chhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCcee
Confidence            4568999999999999999999999997543211      1222233468999999999999999995 99999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecC
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDR  330 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~-v~i~~~~  330 (435)
                      +|..+....                            .......+|||+||.+.++|..|.+.|+.||.+.. -.|++++
T Consensus        82 rv~kas~~~----------------------------~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~  133 (203)
T KOG0131|consen   82 RVNKASAHQ----------------------------KNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDP  133 (203)
T ss_pred             EEEeccccc----------------------------ccccccccccccccCcchhHHHHHHHHHhccccccCCcccccc
Confidence            998765221                            11122368999999999999999999999999754 4789999


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      .||+++|||||.|.+.+.+.+|+.++||..++.++|+|.|+..+..
T Consensus       134 ~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  134 DTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             cCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCC
Confidence            9999999999999999999999999999999999999999977643

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.93  E-value=9.9e-25  Score=217.61  Aligned_cols=190  Identities=18%  Similarity=0.211  Sum_probs=139.7

Q ss_pred             cccCCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ....++|||+|||+ .+|+++|+++|+.||.|            ..+++. ..+|||||+|.+.++|..|+ .|||..|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V------------~~vki~~~~~g~afV~f~~~~~A~~Ai~~lng~~l~  339 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNV------------ERVKFMKNKKETALIEMADPYQAQLALTHLNGVKLF  339 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCe------------EEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            44678999999998 69999999999999984            344433 24799999999999999999 69999999


Q ss_pred             CceEEEcCCCCCCcchhhcCC--CCCCC-CCccccccc-cc----cCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC
Q 013837          248 GVAVRVRRPTDYNPTLAAALG--PGQPS-PNLNLAAVG-LA----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG  319 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~-~~----~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  319 (435)
                      |++|.|.++............  ..... ......... ..    ........+..+|||+|||..+|+++|+++|+.||
T Consensus       340 g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G  419 (481)
T TIGR01649       340 GKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENG  419 (481)
T ss_pred             CceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcC
Confidence            999999987543221111000  00000 000000000 00    00001124567899999999999999999999999


Q ss_pred             C--eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE------EEEEEccCC
Q 013837          320 T--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT------LTVRRATAS  374 (435)
Q Consensus       320 ~--v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~------l~V~~a~~~  374 (435)
                      .  |..|++.... ++ .+|+|||+|.+.++|.+||..|||..|.|+.      |+|.|+++.
T Consensus       420 ~~~i~~ik~~~~~-~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       420 VHKVKKFKFFPKD-NE-RSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             CccceEEEEecCC-CC-cceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            8  8888876543 23 5789999999999999999999999999884      999999653

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=2.4e-25  Score=189.96  Aligned_cols=168  Identities=20%  Similarity=0.351  Sum_probs=151.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..-..|+|.-||..+|+++|+.+|...|+|..|+      .|.+..++.+-||+||.|-++++|++|+ .|||..|..+.
T Consensus        39 ~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScK------LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KT  112 (360)
T KOG0145|consen   39 ESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCK------LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKT  112 (360)
T ss_pred             cccceeeeeecccccCHHHHHHHhhcccceeeee------eeeccccccccccceeeecChHHHHHHHhhhcceeeccce
Confidence            3445699999999999999999999999998765      4788889999999999999999999999 69999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                      |+|.|+.+..                             .......|||.+||..+|..+|.++|++||.|..-+|..|.
T Consensus       113 IKVSyARPSs-----------------------------~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dq  163 (360)
T KOG0145|consen  113 IKVSYARPSS-----------------------------DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQ  163 (360)
T ss_pred             EEEEeccCCh-----------------------------hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhc
Confidence            9999976432                             22334589999999999999999999999999999999998


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe--EEEEEEccCC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK--TLTVRRATAS  374 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~--~l~V~~a~~~  374 (435)
                      .||.++|.+||.|....+|+.||..|||.+-.|+  +|.|+||+..
T Consensus       164 vtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  164 VTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             ccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            8999999999999999999999999999988764  7999999765

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=8.8e-25  Score=186.53  Aligned_cols=197  Identities=25%  Similarity=0.394  Sum_probs=152.0

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc-
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV-  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~-  249 (435)
                      -....|||.+||..+|..+|.++|.+||.|+-.      .++.+..++.++|.+||.|...++|+.|+ .|||+.-.|. 
T Consensus       125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItS------RiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~t  198 (360)
T KOG0145|consen  125 IKDANLYVSGLPKTMTQKELEQIFSPFGRIITS------RILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCT  198 (360)
T ss_pred             hcccceEEecCCccchHHHHHHHHHHhhhhhhh------hhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCC
Confidence            445679999999999999999999999998653      23566667889999999999999999999 6999988774 


Q ss_pred             -eEEEcCCCCCCcchhhc-----C--------CCCCCCCC-c---c----cccc-ccc----------c--CCCCCCCCC
Q 013837          250 -AVRVRRPTDYNPTLAAA-----L--------GPGQPSPN-L---N----LAAV-GLA----------S--GAIGGAEGP  294 (435)
Q Consensus       250 -~l~v~~~~~~~~~~~~~-----~--------~~~~~~~~-~---~----~~~~-~~~----------~--~~~~~~~~~  294 (435)
                       +|.|+++..........     .        ++...... .   +    ..+. ...          .  .........
T Consensus       199 epItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g  278 (360)
T KOG0145|consen  199 EPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGG  278 (360)
T ss_pred             CCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCe
Confidence             79999876543221110     0        00000000 0   0    0000 000          0  011122335


Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      -||||-||.++++|.-|.++|.+||.|..|+|++|..|.++|||+||.+.+.++|..||..|||..++++.|.|.|.+.+
T Consensus       279 ~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  279 WCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             eEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999998654

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=1.6e-25  Score=209.43  Aligned_cols=191  Identities=18%  Similarity=0.268  Sum_probs=147.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      .||||++||+.++.++|.++|+.+|.|.++++      |.+.-...++||+||.|+=.++++.|+ +.++..|.|+.|.|
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~v------Vt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v   79 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVV------VTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNV   79 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEE------ecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccc
Confidence            79999999999999999999999999876531      223334467899999999999999999 69999999999999


Q ss_pred             cCCCCCCcchhhcCCC-CCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          254 RRPTDYNPTLAAALGP-GQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       254 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      ..+...........+. ........    ...+.......+.-.|+|+|||+.|...+|+.+|+.||.|..|.|+..+++
T Consensus        80 ~~A~~R~r~e~~~~~e~~~veK~~~----q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dg  155 (678)
T KOG0127|consen   80 DPAKKRARSEEVEKGENKAVEKPIE----QKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDG  155 (678)
T ss_pred             ccccccccchhcccccchhhhcccc----cCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCC
Confidence            9877654332111100 00000000    000001111223457999999999999999999999999999999988765


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      +. .|||||+|.+..+|..||+.+||..|+|++|.|.||..+..
T Consensus       156 kl-cGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~  198 (678)
T KOG0127|consen  156 KL-CGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDT  198 (678)
T ss_pred             Cc-cceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccccc
Confidence            44 59999999999999999999999999999999999988763

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.93  E-value=5.3e-25  Score=207.21  Aligned_cols=186  Identities=19%  Similarity=0.218  Sum_probs=133.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      ..|||+||.+++++++|+.+|++||.|-.      ++...+..++.++||+||+|.+.++|.+|+ .|||+.|.|+.|+|
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~------v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV  352 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIEN------VQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKV  352 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCccccee------eeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEE
Confidence            34999999999999999999999999733      334555568999999999999999999998 69999999999999


Q ss_pred             cCCCCCCcchhhcCCC---------CCCCCCcc-----------------------ccccc-------cc----cCCCCC
Q 013837          254 RRPTDYNPTLAAALGP---------GQPSPNLN-----------------------LAAVG-------LA----SGAIGG  290 (435)
Q Consensus       254 ~~~~~~~~~~~~~~~~---------~~~~~~~~-----------------------~~~~~-------~~----~~~~~~  290 (435)
                      ...++.......+...         ..+....+                       +.+..       ..    ......
T Consensus       353 ~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p  432 (549)
T KOG0147|consen  353 SVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDP  432 (549)
T ss_pred             EEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCc
Confidence            7554332221110000         00000000                       00000       00    001111


Q ss_pred             C-------CCCCeEEEcCCCCC--CC--------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHH
Q 013837          291 A-------EGPDRVFVGGLPYY--FT--------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (435)
Q Consensus       291 ~-------~~~~~l~V~nLp~~--~t--------e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al  353 (435)
                      .       .++.|+.+.|+-..  .|        .+||.+.|.+||+|..|.+.+.     +-|+.||.|.+++.|..|+
T Consensus       433 ~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~  507 (549)
T KOG0147|consen  433 ADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAV  507 (549)
T ss_pred             cccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHH
Confidence            1       45678889998433  22        2789999999999976666443     3499999999999999999


Q ss_pred             HHhCCceeCCeEEEEEEc
Q 013837          354 AALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       354 ~~l~g~~~~g~~l~V~~a  371 (435)
                      .+|||.||.|+.|++.|.
T Consensus       508 ~alhgrWF~gr~Ita~~~  525 (549)
T KOG0147|consen  508 KALHGRWFAGRMITAKYL  525 (549)
T ss_pred             HHHhhhhhccceeEEEEe
Confidence            999999999999999997

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.93  E-value=1.2e-24  Score=203.70  Aligned_cols=191  Identities=26%  Similarity=0.358  Sum_probs=145.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-----CCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-----~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      +-..|+|+|||+.+.+.+|..+|+.||.|            +.+.++.     -.|||||.|....+|..|| .+|+..|
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V------------~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i  183 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKV------------VEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKI  183 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceE------------EEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCcee
Confidence            35789999999999999999999999984            4444432     3599999999999999999 5999999


Q ss_pred             cCceEEEcCCCCCCcchhhcCC-----------------CCCCC---------------C--Ccccc-------------
Q 013837          247 EGVAVRVRRPTDYNPTLAAALG-----------------PGQPS---------------P--NLNLA-------------  279 (435)
Q Consensus       247 ~g~~l~v~~~~~~~~~~~~~~~-----------------~~~~~---------------~--~~~~~-------------  279 (435)
                      .|++|.|.|+.+...-...+..                 .....               .  ..+.-             
T Consensus       184 ~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~  263 (678)
T KOG0127|consen  184 DGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEED  263 (678)
T ss_pred             cCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhcccccccccc
Confidence            9999999998754432211100                 00000               0  00000             


Q ss_pred             cc-cc-ccC------------CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC
Q 013837          280 AV-GL-ASG------------AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD  345 (435)
Q Consensus       280 ~~-~~-~~~------------~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~  345 (435)
                      .. .. .++            .........+|||+|||+.+|+++|.++|++||.|..+.|+.++.||.++|.|||.|.+
T Consensus       264 ~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt  343 (678)
T KOG0127|consen  264 DVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKT  343 (678)
T ss_pred             ccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEecc
Confidence            00 00 000            01112234789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHh-----CC-ceeCCeEEEEEEccCCC
Q 013837          346 PAVTDIACAAL-----NG-LKMGDKTLTVRRATASS  375 (435)
Q Consensus       346 ~~~A~~Al~~l-----~g-~~~~g~~l~V~~a~~~~  375 (435)
                      ..+|+.||.+.     .| ..|.|+.|+|..|....
T Consensus       344 ~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~Rk  379 (678)
T KOG0127|consen  344 QIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVTRK  379 (678)
T ss_pred             HHHHHHHHHhcCccCCCceEEEeccEEeeeeccchH
Confidence            99999999976     24 78899999999996654

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.92  E-value=2e-25  Score=193.63  Aligned_cols=148  Identities=24%  Similarity=0.433  Sum_probs=133.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      -+|||+|||..+++.+|+.+|++||+|+.|            .+.  |.||||..++...|..|+ .|++.+|+|..|.|
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlEC------------DIv--KNYgFVHiEdktaaedairNLhgYtLhg~nInV   68 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLEC------------DIV--KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINV   68 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEee------------eee--cccceEEeecccccHHHHhhcccceecceEEEE
Confidence            369999999999999999999999996554            332  579999999999999999 59999999999999


Q ss_pred             cCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC
Q 013837          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (435)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg  333 (435)
                      +-++..                               ....++|+|+||.+.++.++|+..|++||+|.++.|+++    
T Consensus        69 eaSksK-------------------------------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd----  113 (346)
T KOG0109|consen   69 EASKSK-------------------------------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD----  113 (346)
T ss_pred             Eecccc-------------------------------CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc----
Confidence            966543                               244578999999999999999999999999999999886    


Q ss_pred             CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       334 ~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                          |+||.|.-.++|..||..|+|.+|.|+.++|++++...
T Consensus       114 ----y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  114 ----YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             ----eeEEEEeeccchHHHHhcccccccccceeeeeeecccc
Confidence                99999999999999999999999999999999987653

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=3.4e-24  Score=191.16  Aligned_cols=182  Identities=27%  Similarity=0.389  Sum_probs=152.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      +-.-.|+|||+.|.+.+.|+.|+..|.+||.|.++++      -.+..+++++|||||||+-+|.|..|+ .|||..++|
T Consensus       109 ALaiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInM------SWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGG  182 (544)
T KOG0124|consen  109 ALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINM------SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGG  182 (544)
T ss_pred             HHHHhHheeeeeeEEEechHHHHhhccCCCCcceeec------ccccccccccceEEEEEeCcHHHHHHHHHhccccccC
Confidence            3455699999999999999999999999999876543      345567889999999999999999999 599999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~  328 (435)
                      +.|+|.++......        ++--.          .-..+....+.|||..+.++++|+||+.+|+.||.|+.|.+.+
T Consensus       183 RNiKVgrPsNmpQA--------QpiID----------~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr  244 (544)
T KOG0124|consen  183 RNIKVGRPSNMPQA--------QPIID----------MVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLAR  244 (544)
T ss_pred             ccccccCCCCCccc--------chHHH----------HHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeec
Confidence            99999976543211        00000          0001123456899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       329 ~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++.++.++||+||+|.+...-..||..||=+.++|..|+|..+...+
T Consensus       245 ~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP  291 (544)
T KOG0124|consen  245 APTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  291 (544)
T ss_pred             cCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccCCC
Confidence            99888999999999999999999999999999999999999886543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.87  E-value=3.7e-22  Score=193.13  Aligned_cols=174  Identities=21%  Similarity=0.378  Sum_probs=141.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ++|||.||++.+|.++|...|...|.|+.+.       |....-    -.+.|||||+|.++++|+.|+ .|+|..|.|+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~-------I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH  588 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIE-------ISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGH  588 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEE-------EeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCc
Confidence            3499999999999999999999999865421       111111    124599999999999999999 6999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      .|.|.++....   +.+.+.                 ........++|+|+|||+.++-.+|+++|..||.|.+|+|++.
T Consensus       589 ~l~lk~S~~k~---~~~~gK-----------------~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK  648 (725)
T KOG0110|consen  589 KLELKISENKP---ASTVGK-----------------KKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKK  648 (725)
T ss_pred             eEEEEeccCcc---cccccc-----------------ccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchh
Confidence            99999876111   101110                 0011122578999999999999999999999999999999998


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ...+.++|||||+|-++.+|..|+.+|.+..|.|+.|.++||+...
T Consensus       649 ~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  649 IGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             hcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhccch
Confidence            6667789999999999999999999999999999999999996654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.87  E-value=1.9e-21  Score=184.48  Aligned_cols=151  Identities=21%  Similarity=0.364  Sum_probs=134.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      .|||+   +++|+..|.++|+++|.++..      .++.+. +  +-|||||.|.++++|.+|| ++|...+.|++|.|.
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~------rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim   70 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSI------RVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIM   70 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeE------EEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEee
Confidence            58999   999999999999999998763      223334 3  8999999999999999999 699999999999999


Q ss_pred             CCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC
Q 013837          255 RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN  334 (435)
Q Consensus       255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~  334 (435)
                      |.....                                  ..|||.||+..++..+|.++|+.||.|++|++..+.+ | 
T Consensus        71 ~s~rd~----------------------------------~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-  114 (369)
T KOG0123|consen   71 WSQRDP----------------------------------SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-  114 (369)
T ss_pred             hhccCC----------------------------------ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-
Confidence            865321                                  1299999999999999999999999999999999964 6 


Q ss_pred             cceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          335 SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       335 ~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++|| ||+|+++++|.+||+.|||..+.|+.|.|.....+.
T Consensus       115 ~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen  115 SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            8999 999999999999999999999999999999886543

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.86  E-value=1.4e-21  Score=168.27  Aligned_cols=141  Identities=27%  Similarity=0.445  Sum_probs=116.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      +..++||||+||...+||+-|..||++.|.+..+++                     .|.                   .
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~---------------------i~~-------------------e   42 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKV---------------------IFD-------------------E   42 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhcccccccee---------------------ehh-------------------h
Confidence            356799999999999999999999999998654321                     111                   4


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                      |+|.|+....         .+..               ......-.+||+.|...++-++|++.|.+||.|.+++|++|.
T Consensus        43 ~~v~wa~~p~---------nQsk---------------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~   98 (321)
T KOG0148|consen   43 LKVNWATAPG---------NQSK---------------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDM   98 (321)
T ss_pred             hccccccCcc---------cCCC---------------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecc
Confidence            5666654321         0111               111224469999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      .|+++|||+||.|.+.++|+.||..|||.+|+++.|+..||+-|+
T Consensus        99 ~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen   99 NTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             cCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCc
Confidence            999999999999999999999999999999999999999998776

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=1.3e-20  Score=180.26  Aligned_cols=187  Identities=17%  Similarity=0.254  Sum_probs=141.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|+|++||..+++.++.+++..||.+..+.      .+.+..++.++||||.+|.++..+..|+ .|||+.++++
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~------lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~  359 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFR------LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDK  359 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhhe------eecccccccccceeeeeeeCCcchhhhhcccchhhhcCc
Confidence            35668899999999999999999999999988765      4777777899999999999999999999 5999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccc--c-cccc-CCCCCCCCCCeEEEcCCC--CCC-C-------HHHHHHHH
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAA--V-GLAS-GAIGGAEGPDRVFVGGLP--YYF-T-------ETQIKELL  315 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~-~~~~~~~~~~~l~V~nLp--~~~-t-------e~~l~~~F  315 (435)
                      +|.|+.+........         ...+..+  . ++.. .......++..|++.|+-  ..+ .       -|+|+..|
T Consensus       360 ~lvvq~A~~g~~~~~---------~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec  430 (500)
T KOG0120|consen  360 KLVVQRAIVGASNAN---------VNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTEC  430 (500)
T ss_pred             eeEeehhhccchhcc---------ccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHh
Confidence            999998764432221         1111000  0 0000 012233445566666652  111 1       16778889


Q ss_pred             HhcCCeeEEEEeec-CC--CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          316 ESFGTLHGFDLVKD-RD--TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       316 ~~~G~v~~v~i~~~-~~--tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .+||.|..|.|+.+ .+  ..-..|..||+|.+.+++++|+.+|+|.+|+|++|...|-.
T Consensus       431 ~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  431 AKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             cccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            99999999999887 21  23355789999999999999999999999999999999974

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=4e-21  Score=164.88  Aligned_cols=83  Identities=28%  Similarity=0.503  Sum_probs=79.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..|+|||-.||.+..+.+|..+|-+||.|.+.+++.|+.|+.+|+|+||.|+++.+|+.||.+|||+.|+-+.|+|.+..
T Consensus       284 eGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLKR  363 (371)
T KOG0146|consen  284 EGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLKR  363 (371)
T ss_pred             CcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhcC
Confidence            45889999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ++.
T Consensus       364 Pkd  366 (371)
T KOG0146|consen  364 PKD  366 (371)
T ss_pred             ccc
Confidence            764

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.85  E-value=1.2e-21  Score=179.11  Aligned_cols=175  Identities=22%  Similarity=0.387  Sum_probs=151.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..++|||++|++.++++.|+++|.+||+|+.|.      ++.+..+++++||+||+|.++++..++|....+.|.|+.|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~------vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve   78 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCV------VMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVE   78 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEE------EeccCCCCCcccccceecCCCcchheeecccccccCCcccc
Confidence            678999999999999999999999999987754      24555668899999999999999999998888899999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      +..+.+......                       ........+|||++||..++++++++.|++||.|..+.++.|..+
T Consensus        79 ~k~av~r~~~~~-----------------------~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~  135 (311)
T KOG4205|consen   79 PKRAVSREDQTK-----------------------VGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTT  135 (311)
T ss_pred             ceeccCcccccc-----------------------cccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccc
Confidence            987765432211                       011124568999999999999999999999999999999999999


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCC
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQ  377 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~  377 (435)
                      ..++||+||.|.+++.+.+++. ..-+.|+|+.|.|..|.++...
T Consensus       136 ~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~pk~~~  179 (311)
T KOG4205|consen  136 SRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAIPKEVM  179 (311)
T ss_pred             cccccceeeEeccccccceecc-cceeeecCceeeEeeccchhhc
Confidence            9999999999999999999988 6889999999999999887643

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.84  E-value=4.1e-21  Score=175.39  Aligned_cols=81  Identities=26%  Similarity=0.457  Sum_probs=77.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ...|||.+||.+.-+.+|...|..||.|++.++..|+.||.++.|+||.|++..+|..||.+|||+.|+++.|+|.+...
T Consensus       424 GanlfiyhlPqefgdq~l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~  503 (510)
T KOG0144|consen  424 GANLFIYHLPQEFGDQDLIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRD  503 (510)
T ss_pred             ccceeeeeCchhhhhHHHHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeec
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999755


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      +
T Consensus       504 ~  504 (510)
T KOG0144|consen  504 R  504 (510)
T ss_pred             c
Confidence            4

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.84  E-value=2.6e-20  Score=176.72  Aligned_cols=205  Identities=24%  Similarity=0.386  Sum_probs=160.5

Q ss_pred             CCCCCCCcccccchhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHH
Q 013837          155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE  234 (435)
Q Consensus       155 ~~~~~~~p~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~  234 (435)
                      +....+.|+..|+.+.....  |||.||+..++..+|.++|+.||+|++|.        +...-..++|| ||+|.++++
T Consensus        59 ~~~~~~~~~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g~ilS~k--------v~~~~~g~kg~-FV~f~~e~~  127 (369)
T KOG0123|consen   59 FDVLKGKPIRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFGNILSCK--------VATDENGSKGY-FVQFESEES  127 (369)
T ss_pred             CcccCCcEEEeehhccCCce--eeecCCCcccCcHHHHHHHHhhcCeeEEE--------EEEcCCCceee-EEEeCCHHH
Confidence            45566777777776655443  99999999999999999999999988753        22333338999 999999999


Q ss_pred             HHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHH
Q 013837          235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKE  313 (435)
Q Consensus       235 a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~  313 (435)
                      |.+|+ .+||..+.|++|.|...............                     ....-+.++|.|++..++++.|.+
T Consensus       128 a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~---------------------~~~~~t~v~vk~~~~~~~~~~l~~  186 (369)
T KOG0123|consen  128 AKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE---------------------YKKRFTNVYVKNLEEDSTDEELKD  186 (369)
T ss_pred             HHHHHHHhcCcccCCCeeEEeeccchhhhcccccc---------------------hhhhhhhhheeccccccchHHHHH
Confidence            99999 69999999999999865443221111000                     112235799999999999999999


Q ss_pred             HHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCCCCchHHHHHHHHHHHHH
Q 013837          314 LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHI  393 (435)
Q Consensus       314 ~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~~~~~~~~~~~~~~~~~~  393 (435)
                      +|..||.|..+.++.+. .|.++||+||+|.+.++|..|+..|||..+.+..+.|..+..     +.+....+...+.+.
T Consensus       187 ~f~~~g~i~s~~v~~~~-~g~~~~~gfv~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk-----k~e~~~~l~~~~~~~  260 (369)
T KOG0123|consen  187 LFSAYGSITSVAVMRDS-IGKSKGFGFVNFENPEDAKKAVETLNGKIFGDKELYVGRAQK-----KSEREAELKRKFEQE  260 (369)
T ss_pred             hhcccCcceEEEEeecC-CCCCCCccceeecChhHHHHHHHhccCCcCCccceeeccccc-----chhhHHHHhhhhHhh
Confidence            99999999999999985 477999999999999999999999999999999999999844     444444444444443


Q ss_pred             HHHH
Q 013837          394 AIQK  397 (435)
Q Consensus       394 ~~~~  397 (435)
                      ....
T Consensus       261 ~~~~  264 (369)
T KOG0123|consen  261 FAKR  264 (369)
T ss_pred             hhhc
Confidence            3333

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.84  E-value=1e-19  Score=154.23  Aligned_cols=185  Identities=22%  Similarity=0.308  Sum_probs=145.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          174 ARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ..||||.||+..+..++|+.    +|++||.|+.         |....+.+.+|.|||.|.+.+.|..|+ +|+|..+.|
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ild---------I~a~kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFyg   79 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILD---------ISAFKTPKMRGQAFVVFKETEAASAALRALQGFPFYG   79 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEE---------EEecCCCCccCceEEEecChhHHHHHHHHhcCCcccC
Confidence            34999999999999999888    9999999765         777778889999999999999999999 799999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCC---------------Cccc-----cccccccC-CCCCCCCCCeEEEcCCCCCCC
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSP---------------NLNL-----AAVGLASG-AIGGAEGPDRVFVGGLPYYFT  307 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~---------------~~~~-----~~~~~~~~-~~~~~~~~~~l~V~nLp~~~t  307 (435)
                      +++.|+|++..........+......               ..+.     ......+. ......+...||+.|||..++
T Consensus        80 K~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~  159 (221)
T KOG4206|consen   80 KPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESE  159 (221)
T ss_pred             chhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchh
Confidence            99999999876554443221110000               0000     00000000 122245567899999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEEcc
Q 013837          308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (435)
Q Consensus       308 e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~V~~a~  372 (435)
                      .+.|..+|+.|.....|.++...     .+.|||+|.+...|..|..+|+|..|- ...+.|.|++
T Consensus       160 ~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  160 SEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999999999988753     579999999999999999999999996 8999999884

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.82  E-value=4.9e-19  Score=175.84  Aligned_cols=80  Identities=19%  Similarity=0.281  Sum_probs=67.4

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+.+++++|+++|+.||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .||++.|+|+.|
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svr------l~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~L  276 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQ------LARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL  276 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEE------EEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            457999999999999999999999999875421      1222235668999999999999999999 699999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus       277 rV~kAi~  283 (612)
T TIGR01645       277 RVGKCVT  283 (612)
T ss_pred             EEEecCC
Confidence            9987653

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.79  E-value=3.7e-18  Score=138.91  Aligned_cols=174  Identities=26%  Similarity=0.358  Sum_probs=128.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC---CCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~---~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ...++|||+|||.++-+.+|.++|.+||.|            ..+.+..   .-.||||+|+++.+|+.|+ .-+|..+.
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i------------~~ieLK~r~g~ppfafVeFEd~RDAeDAiygRdGYdyd   71 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRI------------REIELKNRPGPPPFAFVEFEDPRDAEDAIYGRDGYDYD   71 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcce------------EEEEeccCCCCCCeeEEEecCccchhhhhhcccccccC
Confidence            457899999999999999999999999984            4444433   2479999999999999999 69999999


Q ss_pred             CceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCC---CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 013837          248 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA---IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v  324 (435)
                      |+.|.|+++......... -+...     .....+...+.   ...-.....|.|.+||...+++||++++.+.|.|...
T Consensus        72 g~rLRVEfprggr~s~~~-~G~y~-----gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfa  145 (241)
T KOG0105|consen   72 GCRLRVEFPRGGRSSSDR-RGSYS-----GGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFA  145 (241)
T ss_pred             cceEEEEeccCCCccccc-ccccC-----CCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeee
Confidence            999999988755311100 00000     00000000000   0111223579999999999999999999999999888


Q ss_pred             EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEEEE
Q 013837          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVRR  370 (435)
Q Consensus       325 ~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~V~~  370 (435)
                      .+.+|       |++.|+|...|+-.-|+..|....+.  |.+.-+..
T Consensus       146 dv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~seGe~~yirv  186 (241)
T KOG0105|consen  146 DVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRSEGETAYIRV  186 (241)
T ss_pred             eeecc-------cceeeeeeehhhHHHHHHhhccccccCcCcEeeEEe
Confidence            88876       47899999999999999999877663  55444444

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.79  E-value=1.4e-18  Score=143.68  Aligned_cols=85  Identities=22%  Similarity=0.545  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||+.+||++|+++|++||.|..|.|+.++.|+.++|||||+|.+.++|++||+.|||..|.|+.|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      ..+..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.74  E-value=2.5e-17  Score=153.72  Aligned_cols=170  Identities=21%  Similarity=0.254  Sum_probs=132.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ....|.+++||+.+|++||.+||..++.         ...+.....++..|-|||||.+.+++.+||+.+...+..+.|.
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~I---------~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIE   79 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCGI---------ENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIE   79 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCce---------eEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEE
Confidence            4567999999999999999999998852         1223334447788999999999999999999999999999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRD  331 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~-v~i~~~~~  331 (435)
                      |-.+..........               ..   ..........|-+++||+.||++||.++|+..-.|.. |.++.++ 
T Consensus        80 Vf~~~~~e~d~~~~---------------~~---g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-  140 (510)
T KOG4211|consen   80 VFTAGGAEADWVMR---------------PG---GPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-  140 (510)
T ss_pred             EEccCCcccccccc---------------CC---CCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-
Confidence            98654332211000               00   0011123457899999999999999999998866655 5566665 


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.+.|.|||+|++.+.|++||. -|...|+-+-|.|-.+
T Consensus       141 rgR~tGEAfVqF~sqe~ae~Al~-rhre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  141 RGRPTGEAFVQFESQESAEIALG-RHRENIGHRYIEVFRS  179 (510)
T ss_pred             CCCcccceEEEecCHHHHHHHHH-HHHHhhccceEEeehh
Confidence            47799999999999999999999 5888999999999877

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.72  E-value=1.3e-16  Score=155.02  Aligned_cols=191  Identities=20%  Similarity=0.259  Sum_probs=139.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .......|+|+|||..+..++|..+|..||.|            ..+.+....-.|+|+|.++.+|..|+ .|....+..
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i------------~rvllp~~G~~aiv~fl~p~eAr~Afrklaysr~k~  448 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEI------------GRVLLPPGGTGAIVEFLNPLEARKAFRKLAYSRFKS  448 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhccccc------------ceeecCcccceeeeeecCccchHHHHHHhchhhhcc
Confidence            44566889999999999999999999999984            33444444456999999999999999 599999999


Q ss_pred             ceEEEcCCCCCCcchhh-----cCCCCCC---CCCccccccc---cc-cC----C-----CCCCCCCCeEEEcCCCCCCC
Q 013837          249 VAVRVRRPTDYNPTLAA-----ALGPGQP---SPNLNLAAVG---LA-SG----A-----IGGAEGPDRVFVGGLPYYFT  307 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~-----~~~~~~~---~~~~~~~~~~---~~-~~----~-----~~~~~~~~~l~V~nLp~~~t  307 (435)
                      .++.+.|+-.......+     .......   .+........   .. ..    .     .......++|||.||++.+|
T Consensus       449 ~plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt  528 (725)
T KOG0110|consen  449 APLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTT  528 (725)
T ss_pred             CccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccc
Confidence            99988876433222110     0000000   0000000000   00 00    0     01112223499999999999


Q ss_pred             HHHHHHHHHhcCCeeEEEEeecCCCC---CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          308 ETQIKELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       308 e~~l~~~F~~~G~v~~v~i~~~~~tg---~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|..+|.++|.|+.+.|.+.++..   .+.|||||+|.+.++|+.|+..|+|..|.|+.|.|.++.
T Consensus       529 ~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  529 LEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            99999999999999999888775421   255999999999999999999999999999999999998

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.70  E-value=2.4e-16  Score=143.48  Aligned_cols=232  Identities=16%  Similarity=0.155  Sum_probs=153.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEecCHHHHHHHH-HhCCceecC--ce
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEG--VA  250 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-~g~afv~f~~~~~a~~a~-~l~~~~~~g--~~  250 (435)
                      -.++|+|+-+-++-+-|..+|+.||.|+           ..+.+.++ .-.|.|+|.+.+.|..|. .|+|..|..  +.
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~Vl-----------KIiTF~Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCt  219 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVL-----------KIITFTKNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCT  219 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeE-----------EEEEEecccchhhhhhccchhhHHHHHHhccCCcccCceeE
Confidence            4678999999999999999999999863           22333334 446999999999999999 799987743  67


Q ss_pred             EEEcCCCC--------------CCcchhhcCCCCCCCCCc-------cccc------------c-ccccCCCCCCC-CCC
Q 013837          251 VRVRRPTD--------------YNPTLAAALGPGQPSPNL-------NLAA------------V-GLASGAIGGAE-GPD  295 (435)
Q Consensus       251 l~v~~~~~--------------~~~~~~~~~~~~~~~~~~-------~~~~------------~-~~~~~~~~~~~-~~~  295 (435)
                      |+|.+++.              +... ....+..++....       +..+            . ........+.. ...
T Consensus       220 LrId~Sklt~LnvKynndkSRDyTnp-~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~  298 (492)
T KOG1190|consen  220 LRIDFSKLTDLNVKYNNDKSRDYTNP-DLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANV  298 (492)
T ss_pred             EEeehhhcccceeeccccccccccCC-CCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCce
Confidence            77765442              1110 1111111110000       0000            0 00000111111 246


Q ss_pred             eEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          296 RVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       296 ~l~V~nLp-~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .|.|.||. ..+|.+-|..+|..||.|..|+|+..+.     --|+|+|.+...|+.|++.|+|..|.|+.|+|.+++..
T Consensus       299 vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~  373 (492)
T KOG1190|consen  299 VLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHT  373 (492)
T ss_pred             EEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCc
Confidence            78888885 5689999999999999999999998752     46999999999999999999999999999999999877


Q ss_pred             CCCCch--HHHHHHHHHHHHHHHHHHHhhccCCcccCCCCCCCCCCcceeEEeccccc
Q 013837          375 SGQSKT--EQESILAQAQQHIAIQKMALQTSGMNTLGGGMSLFGETLAKVLCLTEMMK  430 (435)
Q Consensus       375 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~v~~l~n~~~  430 (435)
                      .-+.+.  +.+..+...+.+.++.+ +..++..      ......||+..++|.|+..
T Consensus       374 ~vqlp~egq~d~glT~dy~~spLhr-fkkpgsK------N~~ni~PpsatlHlsnip~  424 (492)
T KOG1190|consen  374 NVQLPREGQEDQGLTKDYGNSPLHR-FKKPGSK------NYQNIFPPSATLHLSNIPP  424 (492)
T ss_pred             cccCCCCCCccccccccCCCCchhh-ccCcccc------cccccCCchhheeeccCCc
Confidence            644332  22223333334444444 2233322      2333467888999998863

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=99.68  E-value=1.3e-15  Score=127.90  Aligned_cols=179  Identities=22%  Similarity=0.306  Sum_probs=120.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~----~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      ....-+||||.+||.++...+|+.+|..|--..+        ..+. .+.+    .+-+|||.|.+...|..|+ .|||.
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEg--------slLK-~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGv  100 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEG--------SLLK-YTSKGDQVCKPVAFATFTSHQFALAAMNALNGV  100 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccc--------eeee-eccCCCccccceEEEEecchHHHHHHHHHhcCe
Confidence            3445789999999999999999999998832111        1211 1222    2479999999999999999 79999


Q ss_pred             eec---CceEEEcCCCCCCcchhhcC----CCCCCCCCc----------------------------ccccc--------
Q 013837          245 IFE---GVAVRVRRPTDYNPTLAAAL----GPGQPSPNL----------------------------NLAAV--------  281 (435)
Q Consensus       245 ~~~---g~~l~v~~~~~~~~~~~~~~----~~~~~~~~~----------------------------~~~~~--------  281 (435)
                      .|+   +..|+|+.++..........    ++.......                            +..+.        
T Consensus       101 rFDpE~~stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~  180 (284)
T KOG1457|consen  101 RFDPETGSTLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKS  180 (284)
T ss_pred             eeccccCceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccch
Confidence            996   57788887664432211110    000000000                            00000        


Q ss_pred             -------cc----------ccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEc
Q 013837          282 -------GL----------ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ  344 (435)
Q Consensus       282 -------~~----------~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~  344 (435)
                             ..          ..........+.+|||.||..+|||++|+.+|+.|-....++|--.  .|  -..|||+|+
T Consensus       181 ~~l~a~~~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~  256 (284)
T KOG1457|consen  181 EALSAPDSKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFE  256 (284)
T ss_pred             hhhhhhhhcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHH
Confidence                   00          0001122234468999999999999999999999988766665432  23  347999999


Q ss_pred             CHHHHHHHHHHhCCcee
Q 013837          345 DPAVTDIACAALNGLKM  361 (435)
Q Consensus       345 ~~~~A~~Al~~l~g~~~  361 (435)
                      +.+.|..|+..|+|..|
T Consensus       257 ~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  257 EIEQATDAMNHLQGNLL  273 (284)
T ss_pred             HHHHHHHHHHHhhccee
Confidence            99999999999999887

>PF00076 RRM_1: RNA recognition motif

Probab=99.66  E-value=7e-16  Score=111.96  Aligned_cols=70  Identities=27%  Similarity=0.644  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      |||+|||..+|+++|+++|+.||.|..+.+..+ .++..+|+|||+|.+.++|.+|++.|||..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999997 5788999999999999999999999999999999985

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.66  E-value=4.3e-16  Score=147.29  Aligned_cols=84  Identities=26%  Similarity=0.428  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||+.+|+++|+++|+.||.|+.|+|+.++.|+.++|||||+|.++++|.+||+.|||..|.++.|+|.|
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            34567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      +++.
T Consensus       184 a~p~  187 (346)
T TIGR01659       184 ARPG  187 (346)
T ss_pred             cccc
Confidence            8764

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.65  E-value=5.9e-16  Score=132.03  Aligned_cols=82  Identities=29%  Similarity=0.441  Sum_probs=79.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|-|.||+.+++|.+|.++|.+||.|..|.|.+|++||.++|||||.|.+.++|++||..|||+-+..-.|.|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      ++
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            75

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.65  E-value=3.1e-16  Score=134.73  Aligned_cols=166  Identities=20%  Similarity=0.296  Sum_probs=125.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      ..|||++||+.+.+.+|..||..||.+..            +.+  -.||+||+|.+..+|..|+ .+++..|.|-.+.|
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d------------~~m--k~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vv   67 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPD------------ADM--KNGFGFVEFEDPRDADDAVHDLDGKELCGERLVV   67 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhcccccc------------cee--ecccceeccCchhhhhcccchhcCceecceeeee
Confidence            36999999999999999999999998533            222  2478999999999999999 79999999988888


Q ss_pred             cCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC
Q 013837          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (435)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg  333 (435)
                      .++....-..    +..  .......   ....-.......+.|+|.++...+.+++|.+.|.++|.+....+       
T Consensus        68 e~~r~~~~~~----g~~--~~g~r~~---~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------  131 (216)
T KOG0106|consen   68 EHARGKRRGR----GRP--RGGDRRS---DSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------  131 (216)
T ss_pred             eccccccccc----CCC--CCCCccc---hhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------
Confidence            8876432111    000  0000000   00001111234467999999999999999999999999854443       


Q ss_pred             CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       334 ~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                       ..++|||+|.+.++|..||..|+|..+.|+.|++.+.
T Consensus       132 -~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  132 -RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             -hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence             2568999999999999999999999999999999443

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.63  E-value=4.8e-15  Score=136.00  Aligned_cols=191  Identities=21%  Similarity=0.286  Sum_probs=136.0

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHH-HHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCc
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQV-MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~-G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~  249 (435)
                      ...+.+||.|||+++..++|+++|... |+|..+.       +.....++.+|||.|||+++|.+++|++ ||.+.+.|+
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yve-------Ll~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR  114 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVE-------LLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGR  114 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeee-------eecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCc
Confidence            345679999999999999999999854 4432211       1222346789999999999999999995 999999999


Q ss_pred             eEEEcCCCCCCcchhhcC---------------------------------CCCCCCCC-------cc-----------c
Q 013837          250 AVRVRRPTDYNPTLAAAL---------------------------------GPGQPSPN-------LN-----------L  278 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~---------------------------------~~~~~~~~-------~~-----------~  278 (435)
                      +|.|+-..+.....-...                                 +.......       .+           .
T Consensus       115 ~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~  194 (608)
T KOG4212|consen  115 ELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNY  194 (608)
T ss_pred             eEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhh
Confidence            999985543211100000                                 00000000       00           0


Q ss_pred             cccccc-----cCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHH
Q 013837          279 AAVGLA-----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (435)
Q Consensus       279 ~~~~~~-----~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al  353 (435)
                      ...+.+     +.-.-.+....++||.||.+.+....|++.|.-.|.|..|.+-.+++ |.++|||.++|.++-+|.+||
T Consensus       195 ~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaI  273 (608)
T KOG4212|consen  195 NLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAI  273 (608)
T ss_pred             hcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHH
Confidence            000000     00011233456799999999999999999999999999999999986 799999999999999999999


Q ss_pred             HHhCCceeCCeEEEEEE
Q 013837          354 AALNGLKMGDKTLTVRR  370 (435)
Q Consensus       354 ~~l~g~~~~g~~l~V~~  370 (435)
                      ..|++.-+..++.++.+
T Consensus       274 sml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  274 SMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HhhccCCCccccceeec
Confidence            99988776777777776

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.62  E-value=5e-15  Score=132.92  Aligned_cols=199  Identities=19%  Similarity=0.251  Sum_probs=136.5

Q ss_pred             chhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       167 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      -++..+.-.+|||..+.++.+|+||+..|+.||+|+.|.+      -.......++||+||||.+......|+ .||=+.
T Consensus       203 vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~L------Ar~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFD  276 (544)
T KOG0124|consen  203 VQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL------ARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFD  276 (544)
T ss_pred             HHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEe------eccCCCCCccceeeEEeccccchHHHhhhcchhh
Confidence            3444566789999999999999999999999999776542      223334568999999999999999999 599999


Q ss_pred             ecCceEEEcCCCCCCcchhhcC--------------------------------CC-------------CCCCCCccccc
Q 013837          246 FEGVAVRVRRPTDYNPTLAAAL--------------------------------GP-------------GQPSPNLNLAA  280 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~~~~~~~~--------------------------------~~-------------~~~~~~~~~~~  280 (435)
                      |+|..|.|..+...........                                +.             .++...+....
T Consensus       277 LGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~  356 (544)
T KOG0124|consen  277 LGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAV  356 (544)
T ss_pred             cccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccc
Confidence            9999999976542221100000                                00             00000000000


Q ss_pred             c-----c---------------------------cc------------------cC-------------CC---------
Q 013837          281 V-----G---------------------------LA------------------SG-------------AI---------  288 (435)
Q Consensus       281 ~-----~---------------------------~~------------------~~-------------~~---------  288 (435)
                      .     +                           ..                  +.             +.         
T Consensus       357 ~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlv  436 (544)
T KOG0124|consen  357 MAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLV  436 (544)
T ss_pred             hhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHH
Confidence            0     0                           00                  00             00         


Q ss_pred             ----CCCCCCCeEEEcCC--CCCCC---HHHHHHHHHhcCCeeEEEEeecCCCCCcc----eEEEEEEcCHHHHHHHHHH
Q 013837          289 ----GGAEGPDRVFVGGL--PYYFT---ETQIKELLESFGTLHGFDLVKDRDTGNSK----GYGFCVYQDPAVTDIACAA  355 (435)
Q Consensus       289 ----~~~~~~~~l~V~nL--p~~~t---e~~l~~~F~~~G~v~~v~i~~~~~tg~~~----G~afV~f~~~~~A~~Al~~  355 (435)
                          .-....+.|.++|+  |.+++   +.+|.+.|.+||.|..|.|...+.++.-.    --.||+|....++.+|+.+
T Consensus       437 MqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~A  516 (544)
T KOG0124|consen  437 MQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQA  516 (544)
T ss_pred             HHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHh
Confidence                00123467888998  55554   46899999999999999998876654211    1379999999999999999


Q ss_pred             hCCceeCCeEEEEEEc
Q 013837          356 LNGLKMGDKTLTVRRA  371 (435)
Q Consensus       356 l~g~~~~g~~l~V~~a  371 (435)
                      |+|.+|+|+.|..+.-
T Consensus       517 LdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  517 LDGRFFGGRKVVAEVY  532 (544)
T ss_pred             hccceecCceeehhhh
Confidence            9999999999887653

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=99.61  E-value=4.5e-14  Score=128.80  Aligned_cols=184  Identities=18%  Similarity=0.128  Sum_probs=135.2

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       174 ~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.|.|.||.. .+|.+.|..+|.-||.            |..+++-. .+-.|.|+|.+...|..|+ .|+|+.|.|++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGd------------VqRVkil~nkkd~ALIQmsd~~qAqLA~~hL~g~~l~gk~  364 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGD------------VQRVKILYNKKDNALIQMSDGQQAQLAMEHLEGHKLYGKK  364 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcc------------eEEEEeeecCCcceeeeecchhHHHHHHHHhhcceecCce
Confidence            67899999976 5899999999999998            44454433 4579999999999999999 59999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCC--CCccccccccc-cC---CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPS--PNLNLAAVGLA-SG---AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF  324 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~-~~---~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v  324 (435)
                      |.|.+++...-.....-.+.+..  +..+....... ++   ......++.+|.+.|+|..++||+|+++|..-|.....
T Consensus       365 lrvt~SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vka  444 (492)
T KOG1190|consen  365 LRVTLSKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKA  444 (492)
T ss_pred             EEEeeccCccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEe
Confidence            99999887654433222111110  11111000000 00   11122456789999999999999999999999887554


Q ss_pred             EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-EEEEEEccC
Q 013837          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLTVRRATA  373 (435)
Q Consensus       325 ~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~V~~a~~  373 (435)
                      .....    +.+.+|+++++++|+|..|+..+|.+.+++. .|+|.|++.
T Consensus       445 fkff~----kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  445 FKFFQ----KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             eeecC----CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence            44332    2355999999999999999999999999855 999999864

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=2.1e-15  Score=122.26  Aligned_cols=78  Identities=22%  Similarity=0.444  Sum_probs=72.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+||+..+++.||..+|..||.|..|+|...+     -|||||||+++.+|..|+..|+|..|+|..|+|++++
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            35789999999999999999999999999999998864     6899999999999999999999999999999999986


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      -..
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            553

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.61  E-value=1.5e-14  Score=129.37  Aligned_cols=197  Identities=16%  Similarity=0.136  Sum_probs=134.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE---EecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~---~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      .....|||.|||.++|-+++.++|..+|-|......  +.+.+.+   .-|.-+|-|.|.|...+++..|+ .|++..|.
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t--~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQT--GEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCC--CCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            445569999999999999999999999987543221  1111111   12445799999999999999999 59999999


Q ss_pred             CceEEEcCCCCCCcchhhcCCC-CCCCCCc------ccccccccc--CCCCCCCCCCeEEEcCCCCC----CC-------
Q 013837          248 GVAVRVRRPTDYNPTLAAALGP-GQPSPNL------NLAAVGLAS--GAIGGAEGPDRVFVGGLPYY----FT-------  307 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~~-~~~~~~~------~~~~~~~~~--~~~~~~~~~~~l~V~nLp~~----~t-------  307 (435)
                      |+.|.|..++=.....-..... .......      ........+  .........++|.|.||-..    .+       
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            9999999775221110000000 0000000      000000011  11223345678999998422    23       


Q ss_pred             HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          308 ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       308 e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .++|.+.|++||.|..|.|.-..    +.|.+-|.|.+.++|..||+.|+|++|+|+.|....-.-+
T Consensus       290 kedl~eec~K~G~v~~vvv~d~h----PdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDRH----PDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEeccC----CCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            36788899999999999876432    5789999999999999999999999999999998876443

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.60  E-value=1.8e-15  Score=125.64  Aligned_cols=86  Identities=23%  Similarity=0.420  Sum_probs=80.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ..+....|.|-||-+.+|.++|..+|++||.|-+|.|+.|+-|+.++|||||.|....+|+.|+++|+|..|.|+.|.|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            34556789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      +|.-..
T Consensus        89 ~arygr   94 (256)
T KOG4207|consen   89 MARYGR   94 (256)
T ss_pred             hhhcCC
Confidence            996554

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=5.1e-15  Score=107.40  Aligned_cols=70  Identities=27%  Similarity=0.580  Sum_probs=65.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      |||+|||..+++++|.++|+.||.|..+.+..+++ |..+|+|||+|.+.++|.+|++.++|..|.|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999977 89999999999999999999999999999999884

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=6.6e-15  Score=130.67  Aligned_cols=86  Identities=28%  Similarity=0.584  Sum_probs=78.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       288 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .......+.|+|.|||+..-+.||+.+|++||.|++|.|+.+.  .-+|||+||.|++.++|.+|-.+|||..+.|+.|.
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            3445667899999999999999999999999999999999973  45799999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |..|+...
T Consensus       168 Vn~ATarV  175 (376)
T KOG0125|consen  168 VNNATARV  175 (376)
T ss_pred             Eeccchhh
Confidence            99997643

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=3.5e-16  Score=127.26  Aligned_cols=80  Identities=34%  Similarity=0.684  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ...|||+|||+.+||.||.-+|++||.|+.|.+++|+.||+++||||+.|++..+...|+.-|||..|.|++|+|..+..
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            34799999999999999999999999999999999999999999999999999999999999999999999999998754

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.59  E-value=1.1e-14  Score=144.73  Aligned_cols=117  Identities=21%  Similarity=0.225  Sum_probs=94.3

Q ss_pred             CHHHHHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHH
Q 013837          231 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTET  309 (435)
Q Consensus       231 ~~~~a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~  309 (435)
                      -.+.|.+|| +++|..+........+..+....                        ........++|||+|||.+++|+
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~------------------------~~~~p~~~~~lFVgnLp~~~tEd   73 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKYGGPPPGW------------------------SGVQPGRGCEVFVGKIPRDLYED   73 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccCCCCCCcc------------------------cCCCCCCCCEEEeCCCCCCCCHH
Confidence            357788888 69999887766666554221100                        00112335789999999999999


Q ss_pred             HHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEEcc
Q 013837          310 QIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (435)
Q Consensus       310 ~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~V~~a~  372 (435)
                      +|.++|++||.|..|+|++| .+|.++|||||+|.+.++|.+||+.||+..|. |+.|.|..+.
T Consensus        74 ~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        74 ELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             HHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            99999999999999999999 78999999999999999999999999999985 7888887664

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.58  E-value=3.8e-15  Score=123.16  Aligned_cols=88  Identities=18%  Similarity=0.357  Sum_probs=73.2

Q ss_pred             chhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       167 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      ........++|||+|||+.+|+++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|+.|+ .||+..
T Consensus        27 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~  100 (144)
T PLN03134         27 LGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAK------VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKE  100 (144)
T ss_pred             cccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEE------EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCE
Confidence            344455678999999999999999999999999875522      2333345678999999999999999999 599999


Q ss_pred             ecCceEEEcCCCCCC
Q 013837          246 FEGVAVRVRRPTDYN  260 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~  260 (435)
                      |.|+.|+|.++....
T Consensus       101 i~Gr~l~V~~a~~~~  115 (144)
T PLN03134        101 LNGRHIRVNPANDRP  115 (144)
T ss_pred             ECCEEEEEEeCCcCC
Confidence            999999999887543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.58  E-value=5.7e-15  Score=113.20  Aligned_cols=80  Identities=25%  Similarity=0.402  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...+||||+||.+.+||+.|.++|+++|.|..|.+-.|+.+..+.|||||+|.+.++|..|+.-++|..+..++|.|.|-
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            34689999999999999999999999999999999899888899999999999999999999999999999999999985

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.57  E-value=1.7e-14  Score=126.57  Aligned_cols=82  Identities=27%  Similarity=0.506  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ++-+||||.-|++.++|.+|+.+|+.||.|+.|.|+.++.||+++|||||+|+++-+...|.+..+|.+|+|+.|.|.+-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            67789999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             cC
Q 013837          372 TA  373 (435)
Q Consensus       372 ~~  373 (435)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            43

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.55  E-value=3.3e-14  Score=125.54  Aligned_cols=75  Identities=21%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||+|||+.+|+++|+++|+.||.|..|.|+.+..   .+|||||+|.+.++|..||. |||..|.|+.|.|.++.
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEecc
Confidence            46899999999999999999999999999999998854   47899999999999999996 99999999999999986

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.54  E-value=3.4e-14  Score=104.71  Aligned_cols=81  Identities=22%  Similarity=0.472  Sum_probs=73.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      +.....|||+|||+.+|.+++.++|.+||.|..|+|-..++   .+|.|||.|+++.+|.+|+..|+|+.+.++.|.|-|
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            34456799999999999999999999999999999987765   489999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      -.+.
T Consensus        92 yq~~   95 (124)
T KOG0114|consen   92 YQPE   95 (124)
T ss_pred             cCHH
Confidence            7443

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=1.6e-14  Score=122.89  Aligned_cols=81  Identities=26%  Similarity=0.537  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+||++.++.++|+..|++||.|++..|+.|+.||++|||+||.|.+.++|.+|++. -.-.|+|++..|.+|.
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            346899999999999999999999999999999999999999999999999999999999984 4578999999999987


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      ..
T Consensus        90 lg   91 (247)
T KOG0149|consen   90 LG   91 (247)
T ss_pred             hc
Confidence            63

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=2e-14  Score=111.17  Aligned_cols=81  Identities=27%  Similarity=0.401  Sum_probs=77.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      -.|||.++...+||++|.+.|..||.|+.|.+-.|.-||-.+|||+|+|++.++|++|+.+|||..|.|..|.|.||..+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus       153 g  153 (170)
T KOG0130|consen  153 G  153 (170)
T ss_pred             C
Confidence            4

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.51  E-value=2.9e-14  Score=116.42  Aligned_cols=82  Identities=27%  Similarity=0.427  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+...+|||+||+..++++.|.++|-+.|+|+.+.|++|+.+...+|||||+|.++|+|.-|++.||..++.|++|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            35567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 013837          371 AT  372 (435)
Q Consensus       371 a~  372 (435)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            97

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.50  E-value=1.2e-14  Score=121.74  Aligned_cols=84  Identities=20%  Similarity=0.400  Sum_probs=80.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||++|...+||.-|...|-+||.|..|.|+.|.++++++|||||+|...|+|.+||..||+.+|.|++|+|.||
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ++-.
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            8754

>PLN03213 repressor of silencing 3; Provisional

Probab=99.50  E-value=8.6e-14  Score=129.77  Aligned_cols=78  Identities=18%  Similarity=0.370  Sum_probs=71.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCH--HHHHHHHHHhCCceeCCeEEEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~--~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....|||+||++.+|++||..+|..||.|..|.|++  +||  +|||||+|.+.  .++.+||..|||..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            346899999999999999999999999999999994  567  99999999987  689999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            9654

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.49  E-value=1.8e-13  Score=134.19  Aligned_cols=78  Identities=19%  Similarity=0.397  Sum_probs=71.5

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ....++||||++|+..++|.||.++|+.||.            |..+.+..++|||||.+....+|.+|| +|++..+.+
T Consensus       417 isV~SrTLwvG~i~k~v~e~dL~~~feefGe------------iqSi~li~~R~cAfI~M~~RqdA~kalqkl~n~kv~~  484 (894)
T KOG0132|consen  417 ISVCSRTLWVGGIPKNVTEQDLANLFEEFGE------------IQSIILIPPRGCAFIKMVRRQDAEKALQKLSNVKVAD  484 (894)
T ss_pred             eeEeeeeeeeccccchhhHHHHHHHHHhccc------------ceeEeeccCCceeEEEEeehhHHHHHHHHHhcccccc
Confidence            4457899999999999999999999999998            677778889999999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|+|.|+..+
T Consensus       485 k~Iki~Wa~g~  495 (894)
T KOG0132|consen  485 KTIKIAWAVGK  495 (894)
T ss_pred             eeeEEeeeccC
Confidence            99999998654

>smart00362 RRM_2 RNA recognition motif

Probab=99.48  E-value=2.8e-13  Score=98.30  Aligned_cols=72  Identities=39%  Similarity=0.691  Sum_probs=67.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      +|+|+|||..+++++|.++|..||.|..+.+..++  +.++|+|||+|.+.++|..|+..++|..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999988875  6788999999999999999999999999999999873

>smart00360 RRM RNA recognition motif

Probab=99.46  E-value=3.4e-13  Score=97.48  Aligned_cols=71  Identities=38%  Similarity=0.700  Sum_probs=67.1

Q ss_pred             EcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          299 VGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       299 V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      |+|||..+++++|+++|+.||.|..+.+..++.++.++|+|||+|.+.++|..|+..|++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999988788999999999999999999999999999999999873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.46  E-value=4.3e-13  Score=116.50  Aligned_cols=75  Identities=15%  Similarity=0.254  Sum_probs=69.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..+|||+||++.+|+++|+++|+.||.|..|.|+.+.   ..+|||||+|.++++|..|+. |||..|.++.|.|....
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            4689999999999999999999999999999999984   456899999999999999996 99999999999999865

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=4.4e-13  Score=123.92  Aligned_cols=84  Identities=26%  Similarity=0.398  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~V~~  370 (435)
                      ...+-|||+.||.++.|++|.-+|++.|.|-+++|++|+.+|.++|||||.|.+.++|+.||+.||+++| .|+.|.|..
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4457899999999999999999999999999999999999999999999999999999999999999999 499999988


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +..+.
T Consensus       161 Svan~  165 (506)
T KOG0117|consen  161 SVANC  165 (506)
T ss_pred             eeecc
Confidence            76554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.44  E-value=1.3e-13  Score=124.69  Aligned_cols=191  Identities=19%  Similarity=0.170  Sum_probs=132.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~--~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      --|-+++||+++|+.++.+||.+-..|.+     ..+.|.-+.-  ++-.|-|||.|..+++|..||.-+...|+.+.|.
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~-----g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIE  236 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTG-----GTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIE  236 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccC-----CccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHH
Confidence            35788999999999999999975433322     1233555543  4567999999999999999998888888888888


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCc-cccccc-cccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeE--EEEe
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNL-NLAAVG-LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHG--FDLV  327 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-v~~--v~i~  327 (435)
                      +.+++...-..........+.... ...... .............||-+++||+.+|.|||.++|..|-. |..  |.++
T Consensus       237 lFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv  316 (508)
T KOG1365|consen  237 LFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMV  316 (508)
T ss_pred             HHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEE
Confidence            876543221111000000000000 000000 00011112233678999999999999999999999875 333  6777


Q ss_pred             ecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          328 KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       328 ~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+. .|.+.|.|||+|.+.+.|.+|....|.....++.|.|--+
T Consensus       317 ~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  317 LNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             EcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            764 4889999999999999999999999988888999998876

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.44  E-value=2.2e-12  Score=118.72  Aligned_cols=74  Identities=23%  Similarity=0.477  Sum_probs=68.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ..++|||+|||+++|++.|++-|..||.|+.+.|+.   .|+++|  .|.|.++++|+.|+..|+|..+.|+.|+|.|.
T Consensus       535 Ka~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  535 KACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            347899999999999999999999999999998844   588887  79999999999999999999999999999984

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.44  E-value=2.2e-13  Score=115.95  Aligned_cols=81  Identities=21%  Similarity=0.409  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~----~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .+..||||.||+..+..++|+.    +|+.||.|++|...+   |.+.+|.|||.|.+.+.|..|+.+|+|+.|.|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            3344999999999999998887    999999998887776   467899999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.||+.+.
T Consensus        84 iqyA~s~s   91 (221)
T KOG4206|consen   84 IQYAKSDS   91 (221)
T ss_pred             eecccCcc
Confidence            99998765

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.43  E-value=3.7e-12  Score=115.09  Aligned_cols=165  Identities=20%  Similarity=0.167  Sum_probs=129.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hCCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~~~~~~g  248 (435)
                      ..+-.|+|++|-..++|.+|.+.++.||.            |..+.....+..|.|+|++.+.|..|+.   -+...+.|
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~------------i~yvt~~P~~r~alvefedi~~akn~Vnfaa~n~i~i~g   96 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGP------------IAYVTCMPHKRQALVEFEDIEGAKNCVNFAADNQIYIAG   96 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCc------------eEEEEeccccceeeeeeccccchhhheehhccCcccccC
Confidence            34557999999999999999999999997            5556666678899999999999999993   56677888


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEE--EcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF--VGGLPYYFTETQIKELLESFGTLHGFDL  326 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~--V~nLp~~~te~~l~~~F~~~G~v~~v~i  326 (435)
                      +...+.+++...-...                      ......+...|.  |-|--+.+|.+-|..+|...|+|..|.|
T Consensus        97 q~Al~NyStsq~i~R~----------------------g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvI  154 (494)
T KOG1456|consen   97 QQALFNYSTSQCIERP----------------------GDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVI  154 (494)
T ss_pred             chhhcccchhhhhccC----------------------CCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEE
Confidence            8888887654321110                      011112223333  4565677999999999999999999988


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEEEEccCCC
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVRRATASS  375 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~V~~a~~~~  375 (435)
                      ++.  +|.   .|.|||++.+.|++|..+|||..|.  -++|+|+||++..
T Consensus       155 fkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP~r  200 (494)
T KOG1456|consen  155 FKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKPTR  200 (494)
T ss_pred             Eec--cce---eeEEeechhHHHHHHHhhcccccccccceeEEEEecCcce
Confidence            875  333   6999999999999999999999884  5899999998764

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.43  E-value=1e-12  Score=122.72  Aligned_cols=169  Identities=23%  Similarity=0.297  Sum_probs=114.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      .++|||+|||..+|+++|.++|..||.+..+.      .+.+..++..+|||||+|.+.++|..|+ .+++..|.|+.|.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~------~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~  188 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR------LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLR  188 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEE------eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeE
Confidence            69999999999999999999999999874421      1233346788999999999999999999 5999999999999


Q ss_pred             EcCCCC-CCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 013837          253 VRRPTD-YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (435)
Q Consensus       253 v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~  331 (435)
                      |.+... ........   .  . ......................+++.+++..++..++..+|..+|.+..+.+.....
T Consensus       189 v~~~~~~~~~~~~~~---~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T COG0724         189 VQKAQPASQPRSELS---N--N-LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKD  262 (306)
T ss_pred             eeccccccccccccc---c--c-cchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCC
Confidence            998653 10000000   0  0 000000000111223334556899999999999999999999999997666665543


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHH
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACA  354 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~  354 (435)
                      ......+.++.+.....+..++.
T Consensus       263 ~~~~~~~~~~~~~~~~~~~~~~~  285 (306)
T COG0724         263 GKIPKSRSFVGNEASKDALESNS  285 (306)
T ss_pred             CcccccccccchhHHHhhhhhhc
Confidence            33333344444444444444443

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.42  E-value=3e-13  Score=103.83  Aligned_cols=85  Identities=22%  Similarity=0.376  Sum_probs=70.1

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceE--EEEecCCCcEEEEEecCHHHHHHHHH-hCCc
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV--NVYINHEKKFAFVEMRTVEEASNAMA-LDGI  244 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~--~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~  244 (435)
                      ..+...++||||+||.+.++|++|.++|..+|.|..+        |+  +..+....|||||+|.+.++|..||. ++|.
T Consensus        30 ~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irri--------iMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgt  101 (153)
T KOG0121|consen   30 LEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRI--------IMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGT  101 (153)
T ss_pred             HHHHhhcceEEEeeeeeeecHHHHHHHHHhccchhee--------EeccccCCcCccceEEEEEecchhHHHHHHHhccC
Confidence            3456789999999999999999999999999986431        21  11233456999999999999999995 9999


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|..++|.|.|...+.
T Consensus       102 rLddr~ir~D~D~GF~  117 (153)
T KOG0121|consen  102 RLDDRPIRIDWDAGFV  117 (153)
T ss_pred             cccccceeeeccccch
Confidence            9999999999876554

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.42  E-value=6.6e-13  Score=117.37  Aligned_cols=78  Identities=26%  Similarity=0.299  Sum_probs=66.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v  253 (435)
                      .++|||+|||+.+|+++|++||+.||.|..         |..+.-...+|||||+|.+.++|..||.|+|..|.|+.|.|
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~---------V~I~~d~~~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~V   74 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEY---------VEMQSENERSQIAYVTFKDPQGAETALLLSGATIVDQSVTI   74 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEE---------EEEeecCCCCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEE
Confidence            579999999999999999999999998543         22122223579999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 013837          254 RRPTDYN  260 (435)
Q Consensus       254 ~~~~~~~  260 (435)
                      .++..+.
T Consensus        75 t~a~~~~   81 (260)
T PLN03120         75 TPAEDYQ   81 (260)
T ss_pred             EeccCCC
Confidence            9887664

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.40  E-value=3e-12  Score=93.33  Aligned_cols=74  Identities=38%  Similarity=0.689  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      +|+|+|||..+++++|.++|..||.|..+.+..++.+ ...|+|||+|.+.++|..|++.+++..+.|+.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999988654 6789999999999999999999999999999999875

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.40  E-value=6.3e-13  Score=127.40  Aligned_cols=81  Identities=36%  Similarity=0.676  Sum_probs=78.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|||+|+|+.+++++|.++|+..|.|.+++++.|++||+.+|||||+|.+.++|..|+..|||.++.|+.|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999999654


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      +
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.39  E-value=7.1e-13  Score=108.34  Aligned_cols=79  Identities=22%  Similarity=0.420  Sum_probs=71.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..+.|||+|||..+-+.+|.++|-+||.|..|.|...+   ..-+||||+|++..+|+.||..-+|..++|+.|+|+|+.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            35789999999999999999999999999999886653   235799999999999999999999999999999999986


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      -.
T Consensus        82 gg   83 (241)
T KOG0105|consen   82 GG   83 (241)
T ss_pred             CC
Confidence            54

>PF13893 RRM_5: RNA recognition motif

Probab=99.39  E-value=1.8e-12  Score=89.27  Aligned_cols=56  Identities=23%  Similarity=0.486  Sum_probs=51.0

Q ss_pred             HHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          311 IKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       311 l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      |.++|++||.|..|.+....     .++|||+|.+.++|..|+..|||..|.|++|+|.||
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999987753     589999999999999999999999999999999996

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>smart00361 RRM_1 RNA recognition motif

Probab=99.38  E-value=2.7e-12  Score=92.66  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=55.2

Q ss_pred             HHHHHHHHH----hcCCeeEEE-EeecCCC--CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          308 ETQIKELLE----SFGTLHGFD-LVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       308 e~~l~~~F~----~~G~v~~v~-i~~~~~t--g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      +++|+++|.    +||.|..|. |+.++.+  +.++|||||+|.+.++|.+|+..|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            577888888    999999995 7777666  889999999999999999999999999999999986

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.36  E-value=3.4e-12  Score=119.10  Aligned_cols=80  Identities=35%  Similarity=0.710  Sum_probs=77.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ..+|||+|||..+|+++|.++|..||.|..|.|..++.+|.++|||||+|.+.++|..|+..++|..|.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58999999999999999999999999999999999988999999999999999999999999999999999999999753

>PF00076 RRM_1: RNA recognition motif

Probab=99.35  E-value=1.8e-12  Score=93.87  Aligned_cols=68  Identities=35%  Similarity=0.535  Sum_probs=56.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCcEEEEEecCHHHHHHHHH-hCCceecCceEE
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAVR  252 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~-~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~l~  252 (435)
                      |||+|||.++|+++|+++|..||.+..+        .+.. ..+..++||||+|.+.++|..|++ ++|..++|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~--------~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESI--------KVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEE--------EEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccc--------cccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999986431        1111 124567999999999999999995 999999999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.35  E-value=4.3e-12  Score=113.03  Aligned_cols=84  Identities=21%  Similarity=0.360  Sum_probs=70.8

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-cCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      .......++|+|.|||+..-+.||+.+|.+||.|++         |..|.- -.+|||+||+|++.++|++|- +|+|..
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~Vld---------VEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~  160 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLD---------VEIIFNERGSKGFGFVTMENPADADRARAELHGTV  160 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceee---------EEEEeccCCCCccceEEecChhhHHHHHHHhhcce
Confidence            344567789999999999999999999999999754         222222 247999999999999999999 799999


Q ss_pred             ecCceEEEcCCCCCC
Q 013837          246 FEGVAVRVRRPTDYN  260 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~  260 (435)
                      +.|++|.|..++...
T Consensus       161 VEGRkIEVn~ATarV  175 (376)
T KOG0125|consen  161 VEGRKIEVNNATARV  175 (376)
T ss_pred             eeceEEEEeccchhh
Confidence            999999999887653

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.34  E-value=1.2e-11  Score=117.04  Aligned_cols=173  Identities=23%  Similarity=0.245  Sum_probs=115.1

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCc---EEEEEecCHHHHHHHHHhCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g---~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      ..-+++|||++||++++|+.|...|..||.++-.+-   .. ......-..+|   |+|+.|+++......|.---..-.
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~VdWP---~k-~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~  331 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVKVDWP---GK-ANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEG  331 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceEeecC---CC-ccccccCCCCCcccEEEEEecchHHHHHHHHHHhhccc
Confidence            356789999999999999999999999998643221   00 00111112355   999999999888877621000111


Q ss_pred             CceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHH-hcCCeeEEEE
Q 013837          248 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE-SFGTLHGFDL  326 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~-~~G~v~~v~i  326 (435)
                      +..++|.-+.......       +.-+ +.+......-......++.+||||++||-.++.++|..+|+ -||.|..+-|
T Consensus       332 ~~yf~vss~~~k~k~V-------QIrP-W~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGI  403 (520)
T KOG0129|consen  332 NYYFKVSSPTIKDKEV-------QIRP-WVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGI  403 (520)
T ss_pred             ceEEEEecCcccccce-------eEEe-eEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEe
Confidence            1222332221111100       0000 00000000111233457788999999999999999999999 7999999999


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHH
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAA  355 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~  355 (435)
                      -.|++-+-++|-|=|.|.+..+-.+||.+
T Consensus       404 DtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  404 DTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             ccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            99988888999999999999999999984

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.33  E-value=1.2e-12  Score=111.55  Aligned_cols=80  Identities=19%  Similarity=0.324  Sum_probs=70.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      .-.+|||+||++.+..++|+++|++||+|+..+      +|.+..++++|||+||+|.+.+.|.+|++-.+-.|+|++..
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eav------vitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aN   84 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAV------VITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKAN   84 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEE------EEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccc
Confidence            346899999999999999999999999998743      46777789999999999999999999998777889999888


Q ss_pred             EcCCCC
Q 013837          253 VRRPTD  258 (435)
Q Consensus       253 v~~~~~  258 (435)
                      ++.+.-
T Consensus        85 cnlA~l   90 (247)
T KOG0149|consen   85 CNLASL   90 (247)
T ss_pred             cchhhh
Confidence            876543

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.32  E-value=1.2e-12  Score=114.64  Aligned_cols=73  Identities=29%  Similarity=0.556  Sum_probs=69.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|||+|||.++++.+|+.+|++||+|++|.|+++        ||||..++...|..||..|||.+|.|..|.|+-++.+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            47999999999999999999999999999999986        9999999999999999999999999999999999877


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        75 s   75 (346)
T KOG0109|consen   75 S   75 (346)
T ss_pred             C
Confidence            3

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.31  E-value=6.4e-12  Score=109.24  Aligned_cols=79  Identities=22%  Similarity=0.213  Sum_probs=67.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ...+|||+||++.+|+++|++||+.||.|..         |..+.-+..++||||+|.++++|..|+.|+|..|.+++|.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~---------V~I~~D~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~   74 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEH---------VEIIRSGEYACTAYVTFKDAYALETAVLLSGATIVDQRVC   74 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEE---------EEEecCCCcceEEEEEECCHHHHHHHHhcCCCeeCCceEE
Confidence            3468999999999999999999999998644         2222234556899999999999999999999999999999


Q ss_pred             EcCCCCCC
Q 013837          253 VRRPTDYN  260 (435)
Q Consensus       253 v~~~~~~~  260 (435)
                      |.....+.
T Consensus        75 It~~~~y~   82 (243)
T PLN03121         75 ITRWGQYE   82 (243)
T ss_pred             EEeCcccc
Confidence            99876654

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=3.4e-12  Score=103.78  Aligned_cols=75  Identities=31%  Similarity=0.437  Sum_probs=64.7

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..++|||+||+..+++.||...|..||.|.            .+.+- ...|||||||+++.+|..|+ .|+|..|.|..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lr------------svWvArnPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r   76 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLR------------SVWVARNPPGFAFVEFEDPRDAEDAVRYLDGKDICGSR   76 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcce------------eEEEeecCCCceEEeccCcccHHHHHhhcCCccccCce
Confidence            468999999999999999999999999753            33332 35699999999999999999 79999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|+.++..
T Consensus        77 ~rVE~S~G~   85 (195)
T KOG0107|consen   77 IRVELSTGR   85 (195)
T ss_pred             EEEEeecCC
Confidence            999976543

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.30  E-value=3.7e-12  Score=109.03  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=73.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.++|-|.||+.+++|++|+++|.+||.|..++      +.++..++.++|||||.|.+.++|.+|+ .|||+-+...-
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvy------lardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LI  260 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVY------LARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLI  260 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeE------EEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEE
Confidence            4678999999999999999999999999986644      3677778999999999999999999999 59999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|+|+++.
T Consensus       261 LrvEwskP~  269 (270)
T KOG0122|consen  261 LRVEWSKPS  269 (270)
T ss_pred             EEEEecCCC
Confidence            999998753

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.27  E-value=1.9e-13  Score=111.47  Aligned_cols=88  Identities=27%  Similarity=0.395  Sum_probs=78.9

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .+...++.-|||+|||+..||.||.-.|++||+|+.++      .|.+..+|.++||||+.|++..+...|+ .|||..|
T Consensus        29 H~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdin------LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki  102 (219)
T KOG0126|consen   29 HQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDIN------LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI  102 (219)
T ss_pred             hhhcccceEEEECCCcccccCCcEEEEeeccCceEEEE------EEecCCCCcccceEEEEecCccceEEEEeccCCcee
Confidence            45567888999999999999999999999999998754      4788889999999999999999999999 6999999


Q ss_pred             cCceEEEcCCCCCCc
Q 013837          247 EGVAVRVRRPTDYNP  261 (435)
Q Consensus       247 ~g~~l~v~~~~~~~~  261 (435)
                      .|+.|+|.....+..
T Consensus       103 ~gRtirVDHv~~Yk~  117 (219)
T KOG0126|consen  103 LGRTIRVDHVSNYKK  117 (219)
T ss_pred             cceeEEeeecccccC
Confidence            999999987766653

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=99.27  E-value=1.3e-10  Score=105.27  Aligned_cols=187  Identities=18%  Similarity=0.190  Sum_probs=129.8

Q ss_pred             cCCeEEEc--CCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec-C
Q 013837          173 HARRVYVG--GLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE-G  248 (435)
Q Consensus       173 ~~~~l~V~--nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g  248 (435)
                      ....|.+.  |--+.+|-+-|..+....|+|+           ..+.+.++.=.|.|||.+.+.|++|. .|||..|. |
T Consensus       119 pN~VLl~TIlNp~YpItvDVly~Icnp~GkVl-----------RIvIfkkngVQAmVEFdsv~~AqrAk~alNGADIYsG  187 (494)
T KOG1456|consen  119 PNKVLLFTILNPQYPITVDVLYTICNPQGKVL-----------RIVIFKKNGVQAMVEFDSVEVAQRAKAALNGADIYSG  187 (494)
T ss_pred             CCeEEEEEeecCccccchhhhhhhcCCCCceE-----------EEEEEeccceeeEEeechhHHHHHHHhhccccccccc
Confidence            33444444  4445689999999999999853           33344445668999999999999999 69998774 3


Q ss_pred             -ceEEEcCCCCCCcchhhc------------CCCCCCCCC---------------ccccc--cc----------------
Q 013837          249 -VAVRVRRPTDYNPTLAAA------------LGPGQPSPN---------------LNLAA--VG----------------  282 (435)
Q Consensus       249 -~~l~v~~~~~~~~~~~~~------------~~~~~~~~~---------------~~~~~--~~----------------  282 (435)
                       ++|+|+|+++..-.....            .++..+..+               .++..  .+                
T Consensus       188 CCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r  267 (494)
T KOG1456|consen  188 CCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSR  267 (494)
T ss_pred             ceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCC
Confidence             789998876422110000            000000000               00000  00                


Q ss_pred             --------cccCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHH
Q 013837          283 --------LASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (435)
Q Consensus       283 --------~~~~~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al  353 (435)
                              .......+..+.+.+.|-+|... ++-+.|..+|-.||.|+.|++++.+     .|.|.||+.+..+.+.|+
T Consensus       268 ~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v  342 (494)
T KOG1456|consen  268 YRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAV  342 (494)
T ss_pred             CccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHH
Confidence                    00011122344578899999865 5778999999999999999999975     468999999999999999


Q ss_pred             HHhCCceeCCeEEEEEEccCCC
Q 013837          354 AALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       354 ~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ..||+..+-|.+|.|.+++...
T Consensus       343 ~hLnn~~lfG~kl~v~~SkQ~~  364 (494)
T KOG1456|consen  343 THLNNIPLFGGKLNVCVSKQNF  364 (494)
T ss_pred             HHhccCccccceEEEeeccccc
Confidence            9999999999999999986543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=99.27  E-value=7e-11  Score=114.82  Aligned_cols=197  Identities=12%  Similarity=0.065  Sum_probs=140.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      ..+.+.+-+.+++++..+.|+++||...-.       ...++.++ ..+.+ .|-++|+|.....+.+|+.-|...+-.+
T Consensus       308 v~d~~y~~~~gm~fn~~~nd~rkfF~g~~~-------~~~~l~~~-~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R  379 (944)
T KOG4307|consen  308 VSDKYYNNYKGMEFNNDFNDGRKFFPGRNA-------QSTDLSEN-RVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNR  379 (944)
T ss_pred             cchhheeeecccccccccchhhhhcCcccc-------cccchhhh-hcCCCcCCceEEEecCcchHHHHHhcCchhhhhc
Confidence            356678888999999999999999985411       11111222 22333 7999999999999999999999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCcccc-------cccc-ccCCC--CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLA-------AVGL-ASGAI--GGAEGPDRVFVGGLPYYFTETQIKELLESFG  319 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~-~~~~~--~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G  319 (435)
                      .+.|..+.+.....+......++.......       ..+. ..+..  ..-....+|||..||..+++.++.++|...-
T Consensus       380 ~~q~~P~g~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~  459 (944)
T KOG4307|consen  380 PFQTGPPGNLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAA  459 (944)
T ss_pred             ceeecCCCccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhh
Confidence            999987766544333333222221111000       0000 01111  1123356999999999999999999999988


Q ss_pred             CeeE-EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          320 TLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       320 ~v~~-v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      .|++ |.|...+ +++..+.|||+|..++++..|+...+.+.++.+.|+|.-.....+
T Consensus       460 ~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~~~~m  516 (944)
T KOG4307|consen  460 AVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIADYAM  516 (944)
T ss_pred             hhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechhhHHH
Confidence            8877 6666554 678889999999999999999988888999999999988765544

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.25  E-value=3.8e-11  Score=112.87  Aligned_cols=190  Identities=20%  Similarity=0.206  Sum_probs=126.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..-.|-+++||+.||++||.+||...-.+      ..+..+....-++..|-|||+|++.+.|++||.-+...|+.+.|.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv------~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIE  175 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIV------PDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIE  175 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCccc------ccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEE
Confidence            45679999999999999999999976211      111112333445678999999999999999999888889988888


Q ss_pred             EcCCCCCCcchhh-----c---CCCCCC----CCC-------------cc----------------------cc----cc
Q 013837          253 VRRPTDYNPTLAA-----A---LGPGQP----SPN-------------LN----------------------LA----AV  281 (435)
Q Consensus       253 v~~~~~~~~~~~~-----~---~~~~~~----~~~-------------~~----------------------~~----~~  281 (435)
                      |..+.........     .   .++...    ...             ..                      ..    ..
T Consensus       176 vF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~  255 (510)
T KOG4211|consen  176 VFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGR  255 (510)
T ss_pred             eehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCcccccccccccccccc
Confidence            8654311100000     0   000000    000             00                      00    00


Q ss_pred             ccc------------cC-CCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHH
Q 013837          282 GLA------------SG-AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV  348 (435)
Q Consensus       282 ~~~------------~~-~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~  348 (435)
                      ...            .+ ..........+.+++||+..++.+|..+|+..-.+ .|.|-..+ +|+..|-|+|+|.+.++
T Consensus       256 ~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~-dGr~TGEAdveF~t~ed  333 (510)
T KOG4211|consen  256 DPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGP-DGRATGEADVEFATGED  333 (510)
T ss_pred             ccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCC-CCccCCcceeecccchh
Confidence            000            00 00011223678999999999999999999988766 67776664 58999999999999999


Q ss_pred             HHHHHHHhCCceeCCeEEEEEEc
Q 013837          349 TDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       349 A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      |..|+. .++..+..+-|.+-..
T Consensus       334 av~Ams-kd~anm~hrYVElFln  355 (510)
T KOG4211|consen  334 AVGAMG-KDGANMGHRYVELFLN  355 (510)
T ss_pred             hHhhhc-cCCcccCcceeeeccc
Confidence            999998 5778888777666554

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=99.25  E-value=8.3e-11  Score=115.91  Aligned_cols=75  Identities=27%  Similarity=0.483  Sum_probs=70.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      +||||++|+.+++|+||..+|+.||.|.+|.++..      +|+|||.+..-.+|.+|+.+|+...+.++.|+|.||..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            58999999999999999999999999999988764      789999999999999999999999999999999999766


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus       496 G  496 (894)
T KOG0132|consen  496 G  496 (894)
T ss_pred             C
Confidence            4

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.23  E-value=5.2e-11  Score=88.09  Aligned_cols=76  Identities=20%  Similarity=0.243  Sum_probs=67.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC---CCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~---~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ..+-|||.|||+.+|.++..++|..||.            |..+.++.   .+|.|||.|++..+|.+|+ .|+|..+.+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~------------IrQIRiG~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~   84 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGT------------IRQIRIGNTKETRGTAFVVYEDIFDAKKACDHLSGYNVDN   84 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccc------------eEEEEecCccCcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence            4578999999999999999999999997            66777664   5799999999999999999 699999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|-+.+...
T Consensus        85 ryl~vlyyq~~~   96 (124)
T KOG0114|consen   85 RYLVVLYYQPED   96 (124)
T ss_pred             ceEEEEecCHHH
Confidence            999999876543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.22  E-value=1.7e-11  Score=88.70  Aligned_cols=64  Identities=34%  Similarity=0.623  Sum_probs=52.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-----CCcEEEEEecCHHHHHHHHH-hCCceecCce
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-----EKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-----~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~  250 (435)
                      |||+|||+.+++++|.++|..||.|            ..+.+..     .+++|||+|.+.++|..|+. +++..|+|+.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v------------~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~   68 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPV------------EKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRK   68 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBE------------EEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCc------------ceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEE
Confidence            7999999999999999999999863            3444333     37999999999999999995 7779999998


Q ss_pred             EE
Q 013837          251 VR  252 (435)
Q Consensus       251 l~  252 (435)
                      |.
T Consensus        69 l~   70 (70)
T PF14259_consen   69 LR   70 (70)
T ss_dssp             EE
T ss_pred             cC
Confidence            74

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.19  E-value=6.9e-11  Score=99.07  Aligned_cols=83  Identities=31%  Similarity=0.518  Sum_probs=75.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhc-CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESF-GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~-G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .....++|..+|..+.+..|..+|.+| |.|..+++.+++.||+++|||||+|++++.|.-|-+.||++.|.|+.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            344679999999999999999999998 6788888889999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      -.+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7554

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.17  E-value=5.3e-11  Score=107.00  Aligned_cols=83  Identities=19%  Similarity=0.397  Sum_probs=78.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.+.|||-.|.+-+|.+||.-+|+.||+|..|.|++|..||.+-.||||+|++.+++++|.-.|.+..|..+.|.|.|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            35667899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      +..
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            843

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.17  E-value=2.2e-11  Score=94.45  Aligned_cols=84  Identities=24%  Similarity=0.217  Sum_probs=71.8

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .......|||.++...+||++|.+.|..||+|..+.      .-.+-.++..+|||+|+|.+.++|++|+ ++||..|.|
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNih------LNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIH------LNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhccccccee------eccccccccccceeeeehHhHHHHHHHHHhccchhhhC
Confidence            344567899999999999999999999999976532      2345567778999999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      .+|.|.|+-..
T Consensus       142 q~v~VDw~Fv~  152 (170)
T KOG0130|consen  142 QNVSVDWCFVK  152 (170)
T ss_pred             CceeEEEEEec
Confidence            99999987544

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.15  E-value=5e-11  Score=99.46  Aligned_cols=79  Identities=20%  Similarity=0.323  Sum_probs=67.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ...+|.|-||.+-++.++|+.+|++||.|-..+      +-.+-.+..++|||||.|....+|+.|| .|+|.+|+|+.|
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVy------IPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVY------IPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCccccee------cccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            456799999999999999999999999864322      2344556778999999999999999999 699999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      .|+.+.
T Consensus        86 rVq~ar   91 (256)
T KOG4207|consen   86 RVQMAR   91 (256)
T ss_pred             eehhhh
Confidence            998764

>smart00362 RRM_2 RNA recognition motif

Probab=99.15  E-value=2.4e-10  Score=82.62  Aligned_cols=67  Identities=37%  Similarity=0.618  Sum_probs=57.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      +|+|+|||..+++++|.++|..||.+.            .+.+    +..+|+|||+|.+.++|..|+ .+++..+.|+.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~------------~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~   68 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIE------------SVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRP   68 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEE------------EEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEE
Confidence            589999999999999999999999753            3332    335699999999999999999 59999999999


Q ss_pred             EEEc
Q 013837          251 VRVR  254 (435)
Q Consensus       251 l~v~  254 (435)
                      |.|.
T Consensus        69 i~v~   72 (72)
T smart00362       69 LRVE   72 (72)
T ss_pred             EeeC
Confidence            8874

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.15  E-value=8.7e-11  Score=103.52  Aligned_cols=79  Identities=19%  Similarity=0.215  Sum_probs=71.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+-+||||+-|+++++|.+|+..|..||.|..+.      .|.+..++.++|||||+|++..+...|. +.+|++|+|+.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~Ikrir------lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrr  172 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIR------LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRR  172 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEE------EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcE
Confidence            6679999999999999999999999999987643      3677788999999999999999999999 69999999999


Q ss_pred             EEEcCC
Q 013837          251 VRVRRP  256 (435)
Q Consensus       251 l~v~~~  256 (435)
                      |.|.+-
T Consensus       173 i~VDvE  178 (335)
T KOG0113|consen  173 ILVDVE  178 (335)
T ss_pred             EEEEec
Confidence            999753

>PLN03213 repressor of silencing 3; Provisional

Probab=99.14  E-value=8.1e-11  Score=110.22  Aligned_cols=76  Identities=18%  Similarity=0.371  Sum_probs=63.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCH--HHHHHHH-HhCCceecCc
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV--EEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~--~~a~~a~-~l~~~~~~g~  249 (435)
                      ...+||||||++.+|+++|...|..||.|..+.         .+. ...+|||||+|.+.  .++.+|| .|||..|.|+
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVE---------IpR-ETGRGFAFVEMssdddaEeeKAISaLNGAEWKGR   78 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVE---------FVR-TKGRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGG   78 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE---------Eec-ccCCceEEEEecCCcHHHHHHHHHHhcCCeecCc
Confidence            446899999999999999999999999965421         111 12389999999987  6899999 6999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .|+|..+++
T Consensus        79 ~LKVNKAKP   87 (759)
T PLN03213         79 RLRLEKAKE   87 (759)
T ss_pred             eeEEeeccH
Confidence            999998764

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.14  E-value=3e-11  Score=115.94  Aligned_cols=81  Identities=27%  Similarity=0.418  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      +.|||||||+.+++++|.++|...|.|+.+.      .+.+-.++..+||||++|.+.++|..|+ .|||.++.|++|+|
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~------~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v   92 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFR------LVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRV   92 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceee------ecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEe
Confidence            8899999999999999999999999987754      3667778899999999999999999999 59999999999999


Q ss_pred             cCCCCCCc
Q 013837          254 RRPTDYNP  261 (435)
Q Consensus       254 ~~~~~~~~  261 (435)
                      .|+.....
T Consensus        93 ~~~~~~~~  100 (435)
T KOG0108|consen   93 NYASNRKN  100 (435)
T ss_pred             ecccccch
Confidence            99876544

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.13  E-value=2.9e-10  Score=98.50  Aligned_cols=80  Identities=30%  Similarity=0.513  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCce-eC--CeEEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MG--DKTLTVR  369 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~-~~--g~~l~V~  369 (435)
                      ..++|||+-|...-.|+|++.+|..||.|++|.+.+.++ |.+||+|||.|.+..+|+.||..|||.. +-  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            346899999999999999999999999999999999875 9999999999999999999999999974 33  4789999


Q ss_pred             EccC
Q 013837          370 RATA  373 (435)
Q Consensus       370 ~a~~  373 (435)
                      |+..
T Consensus        97 ~ADT  100 (371)
T KOG0146|consen   97 FADT  100 (371)
T ss_pred             eccc
Confidence            9954

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.09  E-value=1.1e-10  Score=117.06  Aligned_cols=165  Identities=19%  Similarity=0.321  Sum_probs=132.1

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .......++||++||+..+++.+|+-.|..+|.|-.+.       |....++....||||.|.+.+.+-.|. ++.+..|
T Consensus       366 ~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VD-------iKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I  438 (975)
T KOG0112|consen  366 LDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVD-------IKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLI  438 (975)
T ss_pred             ccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccc-------cccCCCCcccchhhhhhhccccCcccchhhcCCcc
Confidence            34456789999999999999999999999999863310       122224556689999999999999998 6888777


Q ss_pred             cCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 013837          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (435)
Q Consensus       247 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i  326 (435)
                      ..-.+++.+...                               .....+.++|++|+..+....|..+|..||.|..|.+
T Consensus       439 ~~g~~r~glG~~-------------------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy  487 (975)
T KOG0112|consen  439 GNGTHRIGLGQP-------------------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY  487 (975)
T ss_pred             ccCccccccccc-------------------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeec
Confidence            665555554321                               1244568999999999999999999999999988776


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEccCCCC
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRATASSG  376 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a~~~~~  376 (435)
                      -..      .-||||+|++...|+.|+..|-|..|+|  +.|.|.||..-..
T Consensus       488 ~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  488 RHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             ccC------CcceeeecccCccchhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            543      3499999999999999999999999986  7899999976543

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.07  E-value=6.4e-11  Score=99.62  Aligned_cols=83  Identities=22%  Similarity=0.325  Sum_probs=72.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..-++|||++|...+||.-|...|-+||.|..+.      ...+....+.+|||||+|...++|.+|| .||+.+|.|+.
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIq------iPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~Grt   81 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQ------IPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRT   81 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcc------cccchhcccccceeEEEeeccchhHHHhhcCchhhhccee
Confidence            3568999999999999999999999999976533      2455566788999999999999999999 69999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++.+..
T Consensus        82 irVN~AkP~k   91 (298)
T KOG0111|consen   82 IRVNLAKPEK   91 (298)
T ss_pred             EEEeecCCcc
Confidence            9999887643

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.06  E-value=1.1e-10  Score=107.06  Aligned_cols=178  Identities=17%  Similarity=0.206  Sum_probs=136.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCc-eecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGI-IFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~-~~~g~~  250 (435)
                      ...+++|++++...+.+.++..++..+|..+...      ....-....++|+++|.|...+.+..|+++.+. .+.+..
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~------~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~  159 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDAR------SSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNK  159 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccch------hhhhccccccccceeeccccHHHHHHHHHhhhcccccccc
Confidence            3577899999999999999999999998754321      122223456789999999999999999987774 555555


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEE-EcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVF-VGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      +.....+......                   .............++| |.+|+..+++++|+.+|..+|.|..++++.+
T Consensus       160 ~~~dl~~~~~~~~-------------------~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~  220 (285)
T KOG4210|consen  160 GEKDLNTRRGLRP-------------------KNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTD  220 (285)
T ss_pred             ccCcccccccccc-------------------cchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCC
Confidence            4443332221000                   0000111223344555 9999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ..++.++|||||.|.....+..|+.. +...+.+.++.|.+.....
T Consensus       221 ~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  265 (285)
T KOG4210|consen  221 EESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEPRP  265 (285)
T ss_pred             CCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCCCc
Confidence            99999999999999999999999997 8899999999999987653

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=99.05  E-value=1e-09  Score=98.76  Aligned_cols=83  Identities=27%  Similarity=0.444  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~--------v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ...+.|||.|||..+|.+++.++|++||.|..        |+|..+.+ |..+|-|+|.|-..++...||+.|++..|.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            44567999999999999999999999998753        78888854 9999999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 013837          364 KTLTVRRATASS  375 (435)
Q Consensus       364 ~~l~V~~a~~~~  375 (435)
                      +.|+|+.|+...
T Consensus       211 ~~~rVerAkfq~  222 (382)
T KOG1548|consen  211 KKLRVERAKFQM  222 (382)
T ss_pred             cEEEEehhhhhh
Confidence            999999997643

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=99.04  E-value=5.7e-10  Score=96.24  Aligned_cols=133  Identities=23%  Similarity=0.364  Sum_probs=104.6

Q ss_pred             ecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCe
Q 013837          218 INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDR  296 (435)
Q Consensus       218 ~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (435)
                      -+.-.+++|+.|.....-.++- +-++..+.-.+|++...+....            +.           ...-....-.
T Consensus       136 p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gtswed------------Ps-----------l~ew~~~DfR  192 (290)
T KOG0226|consen  136 PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTSWED------------PS-----------LAEWDEDDFR  192 (290)
T ss_pred             CCccCcccccCcchhhhhhhhccccccccccCcceeeccccccCC------------cc-----------cccCccccce
Confidence            3445789999999877777766 4566666666666654433221            11           0011223358


Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ||.+.|..+++++-|...|.+|-.....++++++-||+++||+||.|.+..++..|+..|+|..++.+.|++.-+.-
T Consensus       193 IfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~w  269 (290)
T KOG0226|consen  193 IFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSEW  269 (290)
T ss_pred             eecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhhH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999886643

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=99.02  E-value=4e-11  Score=100.91  Aligned_cols=137  Identities=23%  Similarity=0.303  Sum_probs=111.7

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC----CCcEEEEEecCHHHHHHHHH-hCCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH----EKKFAFVEMRTVEEASNAMA-LDGII  245 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~----~~g~afv~f~~~~~a~~a~~-l~~~~  245 (435)
                      .+..+||||+|+-..++|+-|.++|-+.|.|            +.+.+..    ...||||+|.++....-|++ +||..
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV------------~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~   73 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPV------------YKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDD   73 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCce------------EEEeCCCCccCCCceeeeecccccchhhhhhhcccch
Confidence            3467899999999999999999999999874            4444432    12499999999999999995 99999


Q ss_pred             ecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcC----CCCCCCHHHHHHHHHhcCCe
Q 013837          246 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGG----LPYYFTETQIKELLESFGTL  321 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----Lp~~~te~~l~~~F~~~G~v  321 (435)
                      +.+..++|++                                          +.++    |...++++.+...|+.-|.+
T Consensus        74 l~~~e~q~~~------------------------------------------r~G~shapld~r~~~ei~~~v~s~a~p~  111 (267)
T KOG4454|consen   74 LEEDEEQRTL------------------------------------------RCGNSHAPLDERVTEEILYEVFSQAGPI  111 (267)
T ss_pred             hccchhhccc------------------------------------------ccCCCcchhhhhcchhhheeeecccCCC
Confidence            9999988863                                          3344    56678999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       322 ~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      ..+++..+.+ |.++.++||.+....+.-.|+....+..+.
T Consensus       112 ~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~  151 (267)
T KOG4454|consen  112 EGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELF  151 (267)
T ss_pred             CCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccCcC
Confidence            9999999865 778889999998877777777766555443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.99  E-value=2.5e-11  Score=121.02  Aligned_cols=151  Identities=23%  Similarity=0.270  Sum_probs=125.7

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ....+++||.||+..+.+.+|...|..+|.+-..      .+++-+..+.-+|+|||+|..++.|.+|++++...+.|+ 
T Consensus       664 ~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~v------qi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK-  736 (881)
T KOG0128|consen  664 IRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVV------QIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGK-  736 (881)
T ss_pred             HHHHHHHHHhhcchhhcCchhhhhcCccchhhhH------HHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhh-
Confidence            3566889999999999999999999999875321      112223344557999999999999999998777666652 


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                                                                  ..|+|.|+|+..|.+.|+.+|.++|.++++.++..+
T Consensus       737 --------------------------------------------~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r  772 (881)
T KOG0128|consen  737 --------------------------------------------ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR  772 (881)
T ss_pred             --------------------------------------------hhhheeCCCCCCchHHHHhhccccCCccccchhhhh
Confidence                                                        268999999999999999999999999999988775


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                       .|+++|.|||.|.++.+|.++.....+..+.-..+.|..+++
T Consensus       773 -~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  773 -AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             -ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence             599999999999999999999988888888877777877554

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.99  E-value=1.5e-10  Score=105.47  Aligned_cols=188  Identities=15%  Similarity=0.049  Sum_probs=126.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      .|.|.||.+.+|.++++.||..+|+|-.+.+...   +-++.+......|||.|.+..++..|..|.+++|-++.|.|-.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~---~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPN---VDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRP   85 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCC---CCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEe
Confidence            6999999999999999999999999876555432   3344445556799999999999999999999999999888864


Q ss_pred             CCCCC-cch-h------hcCCCCCCCCCcc--------------cccccc-----ccCCCCCCCCCCeEEEcCCCCCCCH
Q 013837          256 PTDYN-PTL-A------AALGPGQPSPNLN--------------LAAVGL-----ASGAIGGAEGPDRVFVGGLPYYFTE  308 (435)
Q Consensus       256 ~~~~~-~~~-~------~~~~~~~~~~~~~--------------~~~~~~-----~~~~~~~~~~~~~l~V~nLp~~~te  308 (435)
                      .-+.. +.. +      ....+.+-.+...              .+.+..     +..+........+|+|.+|+..+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l  165 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAIL  165 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcc
Confidence            33221 111 0      0001100000000              000000     0000011112367999999999999


Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       309 ~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .++.++|..+|.|....+.-.    ...-+|.|+|........|+. ++|+.+.-....+..-
T Consensus       166 ~e~~e~f~r~Gev~ya~~ask----~~s~~c~~sf~~qts~~halr-~~gre~k~qhsr~ai~  223 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTASK----SRSSSCSHSFRKQTSSKHALR-SHGRERKRQHSRRAII  223 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhcc----CCCcchhhhHhhhhhHHHHHH-hcchhhhhhhhhhhhc
Confidence            999999999999987766543    234578899999999999998 6888887444444333

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=98.99  E-value=2.8e-09  Score=77.33  Aligned_cols=68  Identities=37%  Similarity=0.569  Sum_probs=58.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-----CCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-----HEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-----~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      +|+|+|||..+++++|.++|..||.|.            .+.+.     ...++|||+|.+.++|..|+ .+++..+.|+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~------------~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~   68 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVE------------SVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGR   68 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEE------------EEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            489999999999999999999998743            33222     24799999999999999999 5999999999


Q ss_pred             eEEEcC
Q 013837          250 AVRVRR  255 (435)
Q Consensus       250 ~l~v~~  255 (435)
                      .|.|.+
T Consensus        69 ~~~v~~   74 (74)
T cd00590          69 PLRVEF   74 (74)
T ss_pred             EEEEeC
Confidence            998863

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>PF13893 RRM_5: RNA recognition motif

Probab=98.94  E-value=1.9e-09  Score=74.07  Aligned_cols=54  Identities=35%  Similarity=0.552  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHhhcCCCCCCCCceEEEEecCCC-cEEEEEecCHHHHHHHH-HhCCceecCceEEEcCC
Q 013837          191 IATFFSQVMTAIGGNSAGPGDAVVNVYINHEK-KFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRP  256 (435)
Q Consensus       191 l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~-g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~  256 (435)
                      |.++|++||.            |..+.+...+ ++|||+|.+.++|..|+ .|||..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~------------V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGE------------VKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-------------EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCccc------------EEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            6789999997            6666666665 99999999999999999 59999999999999863

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.94  E-value=6.5e-09  Score=99.16  Aligned_cols=84  Identities=19%  Similarity=0.360  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||.+|...+-..||+.+|++||+|+..+|+.+.-+--.++|+||.+.+.++|.++|+.||...|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34568999999999999999999999999999999988666667899999999999999999999999999999999998


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      +.-.
T Consensus       483 KNEp  486 (940)
T KOG4661|consen  483 KNEP  486 (940)
T ss_pred             ccCc
Confidence            6543

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.93  E-value=4.3e-09  Score=94.94  Aligned_cols=78  Identities=17%  Similarity=0.377  Sum_probs=68.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHH-hCCceeCCeEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA-LNGLKMGDKTLTV  368 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~-l~g~~~~g~~l~V  368 (435)
                      .....++|||++|-..++|.+|+++|.+||.|..|.+...      +++|||+|.+.++|+.|... +|...|+|..|+|
T Consensus       224 eD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i  297 (377)
T KOG0153|consen  224 EDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKI  297 (377)
T ss_pred             cccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEE
Confidence            3345578999999889999999999999999999998875      56999999999999988764 5777889999999


Q ss_pred             EEccC
Q 013837          369 RRATA  373 (435)
Q Consensus       369 ~~a~~  373 (435)
                      .|..+
T Consensus       298 ~Wg~~  302 (377)
T KOG0153|consen  298 KWGRP  302 (377)
T ss_pred             EeCCC
Confidence            99987

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.93  E-value=4.7e-09  Score=95.60  Aligned_cols=180  Identities=20%  Similarity=0.201  Sum_probs=122.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ....-.|-.++||+..++.+|-.||+..-...+      +..+.....+...|+|.|.|.+.+.-..|++-+.+.+.++.
T Consensus        57 ~~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~g------g~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ry  130 (508)
T KOG1365|consen   57 ADDNVVVRARGLPWQSSDQDIARFFKGLNIANG------GRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRY  130 (508)
T ss_pred             cCcceEEEecCCCCCcccCCHHHHHhhhhcccc------ceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCc
Confidence            344556778899999999999999986633221      22233334456679999999999999999999999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhc----CCeeEEEE
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF----GTLHGFDL  326 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~v~i  326 (435)
                      |.|-.+.....-.-...+ +....            ........-.|-+++||+++|+.||.++|.+-    |.++.|-+
T Consensus       131 ievYka~ge~f~~iagg~-s~e~~------------~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLF  197 (508)
T KOG1365|consen  131 IEVYKATGEEFLKIAGGT-SNEAA------------PFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLF  197 (508)
T ss_pred             eeeeccCchhheEecCCc-cccCC------------CCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEE
Confidence            999766543211100000 00000            00000112346789999999999999999743    23455655


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +..+ .|+..|-|||.|..+++|+.||. .|...|+-+.|.+-.+
T Consensus       198 V~rp-dgrpTGdAFvlfa~ee~aq~aL~-khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  198 VTRP-DGRPTGDAFVLFACEEDAQFALR-KHRQNIGQRYIELFRS  240 (508)
T ss_pred             EECC-CCCcccceEEEecCHHHHHHHHH-HHHHHHhHHHHHHHHH
Confidence            5554 58999999999999999999998 4666676666665544

>smart00360 RRM RNA recognition motif

Probab=98.90  E-value=6e-09  Score=74.83  Aligned_cols=70  Identities=33%  Similarity=0.511  Sum_probs=55.1

Q ss_pred             EcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          179 VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       179 V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      |+|||..+++++|+++|..||.|..+.+      ......+.++|||||+|.+.++|..|+ .+++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i------~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRL------VRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEE------EeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6799999999999999999997533110      000012445789999999999999999 599999999998874

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.88  E-value=1.8e-08  Score=76.16  Aligned_cols=80  Identities=23%  Similarity=0.339  Sum_probs=70.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC----CeEEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG----DKTLTV  368 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~--G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~----g~~l~V  368 (435)
                      +||.|+|||...|.++|.+++...  |...-+.++.|..++.+.|||||.|.+++.|.+..+.++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            589999999999999999988763  56777889999888999999999999999999999999999885    688999


Q ss_pred             EEccCC
Q 013837          369 RRATAS  374 (435)
Q Consensus       369 ~~a~~~  374 (435)
                      .||..+
T Consensus        82 ~yAriQ   87 (97)
T PF04059_consen   82 SYARIQ   87 (97)
T ss_pred             ehhHhh
Confidence            999543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.85  E-value=3.1e-09  Score=97.85  Aligned_cols=86  Identities=27%  Similarity=0.568  Sum_probs=78.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||++|++.++++.|++.|..||.|.++.+++|+.++.++||+||+|++.+...++|. ..-+.|.|+.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            45789999999999999999999999999999999999999999999999999999998887 45688999999999998


Q ss_pred             CCCCCCc
Q 013837          373 ASSGQSK  379 (435)
Q Consensus       373 ~~~~~~~  379 (435)
                      +...+.+
T Consensus        84 ~r~~~~~   90 (311)
T KOG4205|consen   84 SREDQTK   90 (311)
T ss_pred             Ccccccc
Confidence            8764433

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.84  E-value=1.6e-08  Score=89.44  Aligned_cols=83  Identities=24%  Similarity=0.413  Sum_probs=75.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|+|.|||+.|+++||+++|..||.+..+.|..++ .|.+.|.|-|.|...++|.+|++.+||..++|+.|++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            344789999999999999999999999999989888885 6999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ....
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            6553

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.83  E-value=2.5e-08  Score=84.51  Aligned_cols=85  Identities=24%  Similarity=0.337  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC---CeEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTL  366 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~-~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~---g~~l  366 (435)
                      ....+||||.+||.++..-+|..+|..|-..+...|... +....++-+|||.|.+..+|.+|+++|||..|+   +.+|
T Consensus        31 ~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   31 PGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            344689999999999999999999999988777666443 222345679999999999999999999999995   8999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|++|+...
T Consensus       111 hiElAKSNt  119 (284)
T KOG1457|consen  111 HIELAKSNT  119 (284)
T ss_pred             EeeehhcCc
Confidence            999997654

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.78  E-value=1.4e-08  Score=91.75  Aligned_cols=78  Identities=24%  Similarity=0.375  Sum_probs=69.7

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH--hCCcee
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA--LDGIIF  246 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~--l~~~~~  246 (435)
                      ..+....+|||++|-..++|.+|++.|.+||+            |..+.+-..+++|||+|.+.+.|+.|.+  +|...|
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGe------------irsi~~~~~~~CAFv~ftTR~aAE~Aae~~~n~lvI  290 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGE------------IRSIRILPRKGCAFVTFTTREAAEKAAEKSFNKLVI  290 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCC------------eeeEEeecccccceeeehhhHHHHHHHHhhcceeee
Confidence            45567789999999999999999999999998            6666677788999999999999999993  888999


Q ss_pred             cCceEEEcCCCC
Q 013837          247 EGVAVRVRRPTD  258 (435)
Q Consensus       247 ~g~~l~v~~~~~  258 (435)
                      +|+.|+|.|...
T Consensus       291 ~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  291 NGFRLKIKWGRP  302 (377)
T ss_pred             cceEEEEEeCCC
Confidence            999999999876

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.78  E-value=2.6e-09  Score=90.15  Aligned_cols=80  Identities=14%  Similarity=0.197  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||.||-..++|+.|.++|-+.|+|..|.|..+++ ++.+ ||||.|.++....-|++.+||..+.+..|+|++-
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            3346899999999999999999999999999999998865 6677 9999999999999999999999999999999885


Q ss_pred             cC
Q 013837          372 TA  373 (435)
Q Consensus       372 ~~  373 (435)
                      .-
T Consensus        85 ~G   86 (267)
T KOG4454|consen   85 CG   86 (267)
T ss_pred             cC
Confidence            43

>smart00361 RRM_1 RNA recognition motif

Probab=98.76  E-value=2.4e-08  Score=71.90  Aligned_cols=61  Identities=21%  Similarity=0.323  Sum_probs=47.3

Q ss_pred             HHHHHHHHH----HHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          188 EQAIATFFS----QVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       188 ~~~l~~~f~----~~G~i~~~~~~~~~~~v~~~~~--~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      +++|+++|.    .||.|..+.     .++++..+  +.++|||||+|.+.++|..|+ .|||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~-----~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKIN-----KIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEE-----EEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            578999999    999864411     00111122  667999999999999999999 69999999999976

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.76  E-value=2.3e-08  Score=95.96  Aligned_cols=178  Identities=16%  Similarity=0.163  Sum_probs=115.0

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ......++|+|-|||..|++++|..+|..||+|.+         |  ..+....|.+||+|.+..+|+.|+ +|++..+.
T Consensus        70 ~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~---------i--r~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~  138 (549)
T KOG4660|consen   70 EKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIRE---------I--RETPNKRGIVFVEFYDVRDAERALKALNRREIA  138 (549)
T ss_pred             cccCccceEEEEecCCcCCHHHHHHHHHhhcchhh---------h--hcccccCceEEEEEeehHhHHHHHHHHHHHHhh
Confidence            34556789999999999999999999999999644         1  223446799999999999999999 79999999


Q ss_pred             CceEEEcCCCCCCcchhhcCCCCCCCCCccccccc--cccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEE
Q 013837          248 GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG--LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD  325 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~  325 (435)
                      |+.|+-......    .  .+....  ..-+....  .......+ .....++. .|++.....-+...|.-+|.+.. .
T Consensus       139 ~~~~k~~~~~~~----~--~~~~~~--~~~~~~~~~p~a~s~pgg-~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~  207 (549)
T KOG4660|consen  139 GKRIKRPGGARR----A--MGLQSG--TSFLNHFGSPLANSPPGG-WPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-R  207 (549)
T ss_pred             hhhhcCCCcccc----c--chhccc--chhhhhccchhhcCCCCC-CcCCccee-eeccchhhhhhhcchhccCcccc-c
Confidence            999882111100    0  000000  00000000  00001111 11222332 28888877666777777887654 2


Q ss_pred             EeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          326 LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       326 i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .     ++.-.-.-||+|.+..++..++..+ |..+.+....++++.+.
T Consensus       208 ~-----~~~~~hq~~~~~~~~~s~a~~~~~~-G~~~s~~~~v~t~S~~~  250 (549)
T KOG4660|consen  208 E-----TPLLNHQRFVEFADNRSYAFSEPRG-GFLISNSSGVITFSGPG  250 (549)
T ss_pred             c-----ccchhhhhhhhhccccchhhcccCC-ceecCCCCceEEecCCC
Confidence            2     2222336789999998887666644 88888888888888664

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.75  E-value=7.5e-09  Score=93.38  Aligned_cols=81  Identities=15%  Similarity=0.335  Sum_probs=75.0

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+...|||..|.+-+|.++|.-+|+.||.|++|.      +|.+.+++.+-.||||+|.+.+++++|. .|++..|..+.
T Consensus       237 PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sce------VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrR  310 (479)
T KOG0415|consen  237 PPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCE------VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRR  310 (479)
T ss_pred             CCcceEEEEecCCcccccchhhHHhhcccceeee------EEecccccchhheeeeeecchhhHHHHHhhhcceeeccce
Confidence            5668899999999999999999999999999875      5888899999999999999999999999 89999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |+|.+++.
T Consensus       311 IHVDFSQS  318 (479)
T KOG0415|consen  311 IHVDFSQS  318 (479)
T ss_pred             EEeehhhh
Confidence            99988654

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.65  E-value=5.6e-08  Score=93.08  Aligned_cols=79  Identities=23%  Similarity=0.415  Sum_probs=68.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|||+|||.++++.+|+++|..||.|+...|..-.-.++..+||||+|.+.++++.||++ +-..|+++.|.|+-....
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4599999999999999999999999999988876532244448999999999999999996 688999999999987554

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.63  E-value=1e-07  Score=91.24  Aligned_cols=83  Identities=22%  Similarity=0.388  Sum_probs=72.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....+.|||.+|...+-..+|+++|.+||+|++.      .+|.+..+...+.|+||++.+.++|.+|| .|+...|.|+
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGA------KVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGr  475 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGA------KVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGR  475 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceece------eeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcce
Confidence            3567889999999999999999999999999884      34666667777889999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|..++..
T Consensus       476 mISVEkaKNE  485 (940)
T KOG4661|consen  476 MISVEKAKNE  485 (940)
T ss_pred             eeeeeecccC
Confidence            9999977643

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.63  E-value=4.2e-08  Score=87.16  Aligned_cols=82  Identities=22%  Similarity=0.397  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .....+||+|+.+.+|.++|...|+.||.|..+.|+.++.+|.++|||||+|.+.+.++.|+. |+|..|.|..|.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            345689999999999999999999999999999999999888999999999999999999999 9999999999999997


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      ...
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            543

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.58  E-value=4.4e-08  Score=82.42  Aligned_cols=78  Identities=22%  Similarity=0.200  Sum_probs=63.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHH-hhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~-i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..--++|..+|..+.+.+|..+|.+||. ++.+.      .-.+..+|.++|||||+|.+.+.|..|- .||++.|.++-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~r------lsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~l  121 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFR------LSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHL  121 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEE------eecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhe
Confidence            3456999999999999999999999953 22110      0134467899999999999999999999 59999999999


Q ss_pred             EEEcCC
Q 013837          251 VRVRRP  256 (435)
Q Consensus       251 l~v~~~  256 (435)
                      |.+.+.
T Consensus       122 L~c~vm  127 (214)
T KOG4208|consen  122 LECHVM  127 (214)
T ss_pred             eeeEEe
Confidence            998864

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.52  E-value=9.3e-08  Score=82.72  Aligned_cols=71  Identities=30%  Similarity=0.637  Sum_probs=65.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ..|||++||+.+.+.+|..+|..||.|..|.+..        ||+||+|.+..+|..|+..|||..|+|-.+.|+|+..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            3689999999999999999999999998887643        5899999999999999999999999999999999984

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.52  E-value=8.2e-08  Score=92.21  Aligned_cols=71  Identities=18%  Similarity=0.294  Sum_probs=64.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      ....+|+|-|||..+++++|..+|+.||.|..|..-.     ...|.+||+|.++-+|++|+++|++..|.|+.|+
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4567899999999999999999999999998866533     3578999999999999999999999999999998

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.48  E-value=1.2e-08  Score=94.13  Aligned_cols=150  Identities=19%  Similarity=0.313  Sum_probs=118.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCc-eecCceEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGI-IFEGVAVR  252 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~-~~~g~~l~  252 (435)
                      ..+|++||.+.++..+|..+|...-.            -..-.+-...|||||.+.+...|.+|++ ++|. .+.|+.+.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~------------~~~g~fl~k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e   69 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKI------------PGSGQFLVKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQE   69 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccC------------CCCcceeeecceeeccCCchhhhhhhHHhhchhhhhcCceee
Confidence            36899999999999999999986611            1111111235899999999999999994 7774 68899999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-ecCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRD  331 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~-~~~~  331 (435)
                      |.......                               ...+.+-|+|+|...-++.|-.++..||.|+.|... .+.+
T Consensus        70 ~~~sv~kk-------------------------------qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e  118 (584)
T KOG2193|consen   70 VEHSVPKK-------------------------------QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE  118 (584)
T ss_pred             ccchhhHH-------------------------------HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH
Confidence            87654322                               223468999999999999999999999999888653 3333


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      |    -..-|+|.+.+.+..||..|+|..+....++|.|-
T Consensus       119 t----avvnvty~~~~~~~~ai~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  119 T----AVVNVTYSAQQQHRQAIHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             H----HHHHHHHHHHHHHHHHHHhhcchHhhhhhhhcccC
Confidence            2    12347889999999999999999999999999996

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.46  E-value=1.7e-07  Score=85.52  Aligned_cols=84  Identities=23%  Similarity=0.385  Sum_probs=77.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~--------~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ....+|||-+||..+++++|.++|.++|.|.        .|.|.++++|+.+||-|.|.|++...|+.||.-+++..|.|
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            4456899999999999999999999999874        37888999999999999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 013837          364 KTLTVRRATASS  375 (435)
Q Consensus       364 ~~l~V~~a~~~~  375 (435)
                      .+|+|.+|....
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999999997665

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.41  E-value=5.3e-07  Score=88.72  Aligned_cols=84  Identities=18%  Similarity=0.304  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~---tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      ...+++|||+||++.++++.|...|..||+|..|+|+....   ....+-++||-|.+-.+|++|++.|+|..+.+..++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            45567899999999999999999999999999999987642   233556899999999999999999999999999999


Q ss_pred             EEEccCC
Q 013837          368 VRRATAS  374 (435)
Q Consensus       368 V~~a~~~  374 (435)
                      +.|++.-
T Consensus       251 ~gWgk~V  257 (877)
T KOG0151|consen  251 LGWGKAV  257 (877)
T ss_pred             ecccccc
Confidence            9998543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.33  E-value=4.2e-06  Score=74.27  Aligned_cols=84  Identities=15%  Similarity=0.182  Sum_probs=66.1

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .+....+|+|.|||+.++++||+++|..||.+...       .+-....+.+.|.|-|.|...++|..|+ .+++..+.|
T Consensus        79 ~~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~-------~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG  151 (243)
T KOG0533|consen   79 NETRSTKVNVSNLPYGVIDADLKELFAEFGELKRV-------AVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDG  151 (243)
T ss_pred             cCCCcceeeeecCCcCcchHHHHHHHHHhccceEE-------eeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCC
Confidence            34455789999999999999999999999854210       1122234567799999999999999999 699999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|++.......
T Consensus       152 ~~mk~~~i~~~~  163 (243)
T KOG0533|consen  152 RPMKIEIISSPS  163 (243)
T ss_pred             ceeeeEEecCcc
Confidence            999987655443

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.31  E-value=1.1e-06  Score=84.32  Aligned_cols=77  Identities=22%  Similarity=0.336  Sum_probs=63.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~--~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      ....+|||+|||.++++.+|.++|..||.|...        -+.+..  +....||||+|.+..++..|++.+...++++
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~--------~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~  357 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEG--------GIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGR  357 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhccccccc--------ceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCe
Confidence            444569999999999999999999999998653        333433  3334899999999999999998889999999


Q ss_pred             eEEEcCC
Q 013837          250 AVRVRRP  256 (435)
Q Consensus       250 ~l~v~~~  256 (435)
                      +|.|+--
T Consensus       358 kl~Veek  364 (419)
T KOG0116|consen  358 KLNVEEK  364 (419)
T ss_pred             eEEEEec
Confidence            9999743

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.22  E-value=4.2e-06  Score=63.37  Aligned_cols=79  Identities=11%  Similarity=0.167  Sum_probs=59.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec----Cc
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE----GV  249 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~----g~  249 (435)
                      .||+|+|||...|.++|.+++.....  +...  -.=..++.....+.|||||.|.+++.|.... .++|..|.    .+
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~--g~yD--F~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~K   77 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFK--GKYD--FFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKK   77 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhcc--Ccce--EEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCc
Confidence            48999999999999999999987632  1100  0001345556678999999999999999999 69999886    35


Q ss_pred             eEEEcCCC
Q 013837          250 AVRVRRPT  257 (435)
Q Consensus       250 ~l~v~~~~  257 (435)
                      ...|.+|.
T Consensus        78 vc~i~yAr   85 (97)
T PF04059_consen   78 VCEISYAR   85 (97)
T ss_pred             EEEEehhH
Confidence            56776664

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.19  E-value=7.8e-06  Score=58.76  Aligned_cols=69  Identities=13%  Similarity=0.252  Sum_probs=47.6

Q ss_pred             eEEEcCCCCCCCHHH----HHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          296 RVFVGGLPYYFTETQ----IKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       296 ~l~V~nLp~~~te~~----l~~~F~~~G~-v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .|+|.|||.+.+...    |+.++..+|. |..|  .        .|.|+|.|.+.+.|..|.+.|+|..+.|..|.|.|
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            599999999988755    5567777875 5443  1        35799999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      ....
T Consensus        74 ~~~~   77 (90)
T PF11608_consen   74 SPKN   77 (90)
T ss_dssp             S--S
T ss_pred             cCCc
Confidence            8443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.14  E-value=1.4e-06  Score=77.61  Aligned_cols=83  Identities=27%  Similarity=0.295  Sum_probs=70.4

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      +.......+||+|+.+.+|.++|...|+.||.|...      .+..+...+..+|||||+|.+.+.+..|+.|++..|.|
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~------ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~  169 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRV------TVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPG  169 (231)
T ss_pred             hhccCCceEEEeccccccccchhhheeeccCCccce------eeeccccCCCcceeEEEecccHhhhHHHhhcCCccccc
Confidence            456778899999999999999999999999986431      22444455678999999999999999999999999999


Q ss_pred             ceEEEcCCC
Q 013837          249 VAVRVRRPT  257 (435)
Q Consensus       249 ~~l~v~~~~  257 (435)
                      ..+.|.+..
T Consensus       170 ~~i~vt~~r  178 (231)
T KOG4209|consen  170 PAIEVTLKR  178 (231)
T ss_pred             ccceeeeee
Confidence            999998654

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.06  E-value=7.3e-06  Score=80.93  Aligned_cols=85  Identities=20%  Similarity=0.286  Sum_probs=66.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ......|||+||++.++++.|...|..||.|.+..++.+   -....-...+.|+||.|.+..+|..|+ .|+|..+.+.
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwp---RtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWP---RTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecc---cchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            445678999999999999999999999998755332211   011111234689999999999999999 6999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .+++.|.+.
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999999854

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.05  E-value=1.4e-05  Score=78.75  Aligned_cols=77  Identities=17%  Similarity=0.311  Sum_probs=67.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ++.|-+.|+|+.++.+||.++|..|-.+-.-.+++..+.|...|.|.|-|++.++|..|...|++..|..++|.|..
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            34788999999999999999999998764433444446799999999999999999999999999999999998864

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.02  E-value=4.8e-06  Score=75.39  Aligned_cols=79  Identities=24%  Similarity=0.380  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~--v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      -|+||+||-+.+|++||.+.+...|.  |.+++++.+..+|.+||||+|...+.....+.++.|-...|.|..-.|.-.+
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~N  160 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSYN  160 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeeccc
Confidence            47999999999999999999988775  7778888888899999999999999999999999999999999877776654


Q ss_pred             C
Q 013837          373 A  373 (435)
Q Consensus       373 ~  373 (435)
                      +
T Consensus       161 K  161 (498)
T KOG4849|consen  161 K  161 (498)
T ss_pred             h
Confidence            3

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.02  E-value=8.7e-06  Score=63.22  Aligned_cols=71  Identities=23%  Similarity=0.315  Sum_probs=44.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC-----CceeCCeEEEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN-----GLKMGDKTLTVR  369 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~-----g~~~~g~~l~V~  369 (435)
                      +.|+|.+++..++.++|+++|+.||.|..|.+...-      ..|||.|.+.+.|+.|+..+.     +..+.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            468899999999999999999999999988887652      268999999999999998763     446677777666


Q ss_pred             Ec
Q 013837          370 RA  371 (435)
Q Consensus       370 ~a  371 (435)
                      .-
T Consensus        76 vL   77 (105)
T PF08777_consen   76 VL   77 (105)
T ss_dssp             --
T ss_pred             EC
Confidence            53

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=97.99  E-value=8.5e-06  Score=70.90  Aligned_cols=78  Identities=18%  Similarity=0.348  Sum_probs=69.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...-+||.+.|...++.+-|-..|.+|=....      ..+|.+..+++++||+||.|.+..++..|| +|+|..++.++
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~------akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrp  261 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQK------AKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRP  261 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhh------ccccccccccccccceeeeecCHHHHHHHHHhhcccccccch
Confidence            45578999999999999999999999865444      346889999999999999999999999999 79999999999


Q ss_pred             EEEcC
Q 013837          251 VRVRR  255 (435)
Q Consensus       251 l~v~~  255 (435)
                      |++..
T Consensus       262 iklRk  266 (290)
T KOG0226|consen  262 IKLRK  266 (290)
T ss_pred             hHhhh
Confidence            99864

>PF06495 Transformer: Fruit fly transformer protein; InterPro: IPR010519 This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly)

Probab=97.97  E-value=6.7e-05  Score=61.39  Aligned_cols=16  Identities=25%  Similarity=0.378  Sum_probs=13.5

Q ss_pred             CCCccCCCCccCCCCC
Q 013837          111 RSGFDMAPPAAAMLPG  126 (435)
Q Consensus       111 ~~~~~~~p~~~~~~~~  126 (435)
                      ...|++++++|+.+..
T Consensus       116 ~~yv~VPp~gf~~~y~  131 (182)
T PF06495_consen  116 TKYVDVPPPGFEYAYG  131 (182)
T ss_pred             eeeccCCCcccccccC
Confidence            5689999999988765

The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster [].; GO: 0006397 mRNA processing, 0046660 female sex differentiation, 0005634 nucleus

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.96  E-value=2.4e-05  Score=69.34  Aligned_cols=79  Identities=14%  Similarity=0.135  Sum_probs=60.5

Q ss_pred             CeEEEcCC--CCCCC---HHHHHHHHHhcCCeeEEEEeecCCCCCc-ceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          295 DRVFVGGL--PYYFT---ETQIKELLESFGTLHGFDLVKDRDTGNS-KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       295 ~~l~V~nL--p~~~t---e~~l~~~F~~~G~v~~v~i~~~~~tg~~-~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      +.|+++|+  +..+.   ++++.+.|++||.|..|.|...+..-.. .--.||+|+..++|.+|+-.|||..|+|+.+..
T Consensus       282 kvlllrnmVg~gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A  361 (378)
T KOG1996|consen  282 KVLLLRNMVGAGEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSA  361 (378)
T ss_pred             HHHHhhhhcCcccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeh
Confidence            34666666  23343   4678999999999999988876431111 113799999999999999999999999999999


Q ss_pred             EEccC
Q 013837          369 RRATA  373 (435)
Q Consensus       369 ~~a~~  373 (435)
                      .|-+.
T Consensus       362 ~Fyn~  366 (378)
T KOG1996|consen  362 CFYNL  366 (378)
T ss_pred             eeccH
Confidence            98643

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.95  E-value=7.3e-05  Score=53.85  Aligned_cols=71  Identities=23%  Similarity=0.268  Sum_probs=46.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      .|+|.|||.+.+...|+.-+.+.-+=.+       ..|+.+    ..+.|+|.|.+.+.|..|. .|+|..+.|..|.|.
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCG-------GkVl~v----~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCG-------GKVLSV----SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT---------EEE------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccC-------CEEEEE----eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5999999999988776665554433221       236655    3589999999999999999 599999999999999


Q ss_pred             CCC
Q 013837          255 RPT  257 (435)
Q Consensus       255 ~~~  257 (435)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            863

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.91  E-value=4.2e-05  Score=73.84  Aligned_cols=77  Identities=25%  Similarity=0.355  Sum_probs=64.0

Q ss_pred             CCeEEEcCCCCCCCH------HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEE
Q 013837          294 PDRVFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTL  366 (435)
Q Consensus       294 ~~~l~V~nLp~~~te------~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l  366 (435)
                      ..+|+|.|+|.--..      .-|..+|+++|+|..+.++.+.++| ++||+|++|.+..+|..|++.|||+.|. +++.
T Consensus        58 D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf  136 (698)
T KOG2314|consen   58 DSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTF  136 (698)
T ss_pred             ceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceE
Confidence            458999999854221      3466889999999999999887654 8999999999999999999999999986 6777


Q ss_pred             EEEEc
Q 013837          367 TVRRA  371 (435)
Q Consensus       367 ~V~~a  371 (435)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            77654

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.82  E-value=5.8e-07  Score=90.46  Aligned_cols=165  Identities=13%  Similarity=0.085  Sum_probs=115.4

Q ss_pred             ccCCeEEEcCCCCCCCHH-HHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          172 RHARRVYVGGLPPLANEQ-AIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~-~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      -....+.+.++.+..... .....|..+|.+..++..       .-..... ..++++.+.....++.|....+..+.++
T Consensus       569 ~~~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p-------~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~  641 (881)
T KOG0128|consen  569 LERREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGP-------KRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANR  641 (881)
T ss_pred             hhhhhhcccCCCcchhhHHhhHHHhhcccccccccCc-------cccccccccchhhhhhccccchhhcccccccccCCc
Confidence            345567788887776554 677888888875432210       0011112 2388999999999999998888888888


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      .+.|..+...........                   .........++||.||+..+.+++|...|..+|.+..+.|...
T Consensus       642 ~~av~~ad~~~~~~~~kv-------------------s~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h  702 (881)
T KOG0128|consen  642 SAAVGLADAEEKEENFKV-------------------SPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIH  702 (881)
T ss_pred             cccCCCCCchhhhhccCc-------------------CchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHH
Confidence            887775543321110000                   0001112347899999999999999999999999988887766


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      ..++..+|+|||+|...++|.+|+....+..++
T Consensus       703 ~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  703 KNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             hhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            677899999999999999999998855444443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.72  E-value=7.4e-05  Score=67.58  Aligned_cols=81  Identities=16%  Similarity=0.293  Sum_probs=63.0

Q ss_pred             CCeEEEcCCCCCCCHHH----H--HHHHHhcCCeeEEEEeecCCCCC-cceE--EEEEEcCHHHHHHHHHHhCCceeCCe
Q 013837          294 PDRVFVGGLPYYFTETQ----I--KELLESFGTLHGFDLVKDRDTGN-SKGY--GFCVYQDPAVTDIACAALNGLKMGDK  364 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~----l--~~~F~~~G~v~~v~i~~~~~tg~-~~G~--afV~f~~~~~A~~Al~~l~g~~~~g~  364 (435)
                      .+-+||-+||+.+-.|+    |  .++|.+||.|..|.|-+...... .-+.  .||.|.+.++|..||.+.+|..++|+
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            35689999998876665    2  37899999998887765431111 1122  49999999999999999999999999


Q ss_pred             EEEEEEccCC
Q 013837          365 TLTVRRATAS  374 (435)
Q Consensus       365 ~l~V~~a~~~  374 (435)
                      .|+..|.+.+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9999997654

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.71  E-value=3.6e-05  Score=70.64  Aligned_cols=89  Identities=20%  Similarity=0.182  Sum_probs=72.5

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCC--CCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG--PGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~--~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~  247 (435)
                      ....-+|||.+||..+++++|.++|.++|.|.......  -..+-.+..+...|+-|.|.|.+...|+.|+. +++..|.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34566899999999999999999999999886544432  12233455677889999999999999999995 9999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      +.+|+|..+...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999999876543

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.69  E-value=1.9e-05  Score=69.11  Aligned_cols=64  Identities=11%  Similarity=0.227  Sum_probs=53.9

Q ss_pred             HHHHHHHH-hcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          309 TQIKELLE-SFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       309 ~~l~~~F~-~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ++|..+|+ +||.|+.+.|-.+-. -...|-+||+|..+++|++|++.|||.+|.|++|...++..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            66777777 899999887665421 23578899999999999999999999999999999999854

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.66  E-value=0.00025  Score=54.13  Aligned_cols=77  Identities=19%  Similarity=0.260  Sum_probs=51.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEE-EeecC------CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-E
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFD-LVKDR------DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-T  365 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~-i~~~~------~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-~  365 (435)
                      ...|.|-+.|.. ....|.+.|++||.|++.. +..+.      ..........|+|.+..+|.+||. .||..|+|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCcEE
Confidence            357899999988 5667889999999997764 10100      000123478999999999999999 699999875 5


Q ss_pred             EEEEEcc
Q 013837          366 LTVRRAT  372 (435)
Q Consensus       366 l~V~~a~  372 (435)
                      +-|.+++
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            6688874

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.64  E-value=0.00014  Score=48.68  Aligned_cols=52  Identities=17%  Similarity=0.315  Sum_probs=42.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHH
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC  353 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al  353 (435)
                      +.|.|.+.+.... ++|...|..||.|+.+.+...      .-++||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            5788999987755 456668999999999887632      338999999999999985

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.62  E-value=6.5e-05  Score=70.01  Aligned_cols=102  Identities=20%  Similarity=0.281  Sum_probs=74.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCCeEEEEEEcc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTL-HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRAT  372 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v-~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~-~~~g~~l~V~~a~  372 (435)
                      ..||++||.+.++..||..+|...-.- ..-.+++       .|||||.+.+...|.+|++.++|. .+.|+.+.|.++.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k-------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            468999999999999999999865221 1112232       479999999999999999999987 6789999999997


Q ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHhhcc
Q 013837          373 ASSGQSKTEQESILAQAQQHIAIQKMALQTS  403 (435)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (435)
                      ++..+....+-.....+++...+..|..+++
T Consensus        75 ~kkqrsrk~Qirnippql~wevld~Ll~qyg  105 (584)
T KOG2193|consen   75 PKKQRSRKIQIRNIPPQLQWEVLDSLLAQYG  105 (584)
T ss_pred             hHHHHhhhhhHhcCCHHHHHHHHHHHHhccC
Confidence            7654444333333344445555566665554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.48  E-value=0.00024  Score=62.22  Aligned_cols=101  Identities=21%  Similarity=0.252  Sum_probs=82.1

Q ss_pred             HHHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHH
Q 013837          234 EASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIK  312 (435)
Q Consensus       234 ~a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~  312 (435)
                      -|..|. +|++....|+.+.|.|+..                                    ..|+|.||...+..+.|.
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~------------------------------------a~l~V~nl~~~~sndll~   49 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH------------------------------------AELYVVNLMQGASNDLLE   49 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc------------------------------------ceEEEEecchhhhhHHHH
Confidence            455666 6999999999999998653                                    369999999999999999


Q ss_pred             HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC--C--ceeCCeEEEEEEc
Q 013837          313 ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--G--LKMGDKTLTVRRA  371 (435)
Q Consensus       313 ~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g--~~~~g~~l~V~~a  371 (435)
                      ..|..||.|....++.| +.++..+-++|+|...-.|.+|+..++  |  ....+..+.|...
T Consensus        50 ~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   50 QAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             HhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            99999999988777776 357888899999999999999998773  2  2345666666554

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.41  E-value=0.00015  Score=67.85  Aligned_cols=79  Identities=14%  Similarity=0.188  Sum_probs=61.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec---CCCC--Cc--------ceEEEEEEcCHHHHHHHHHHhCC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD---RDTG--NS--------KGYGFCVYQDPAVTDIACAALNG  358 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~---~~tg--~~--------~G~afV~f~~~~~A~~Al~~l~g  358 (435)
                      .+.++|.+.|||.+-.-+-|.++|..+|.|..|+|.+.   ++.+  .+        +-+|||+|+..+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46789999999999888999999999999999999887   3322  22        34699999999999999998765


Q ss_pred             ceeCCeEEEEEE
Q 013837          359 LKMGDKTLTVRR  370 (435)
Q Consensus       359 ~~~~g~~l~V~~  370 (435)
                      ..-+-.-|+|.+
T Consensus       309 e~~wr~glkvkL  320 (484)
T KOG1855|consen  309 EQNWRMGLKVKL  320 (484)
T ss_pred             hhhhhhcchhhh
Confidence            544333333333

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.40  E-value=0.00044  Score=46.32  Aligned_cols=52  Identities=19%  Similarity=0.527  Sum_probs=43.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~  239 (435)
                      +.|-|.|.+....+. |..+|..||+            |.++.......++||+|.+..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGe------------I~~~~~~~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGE------------IVDIYVPESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCC------------EEEEEcCCCCcEEEEEECCHHHHHhhC
Confidence            568899999877654 5568999998            666777777889999999999999986

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.34  E-value=0.00048  Score=53.48  Aligned_cols=68  Identities=22%  Similarity=0.254  Sum_probs=42.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hC---CceecC
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LD---GIIFEG  248 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~---~~~~~g  248 (435)
                      +.|+|.+++..++-++|++.|..||.            |..|.+......|||.|.+.+.|..|++   ..   +..+.+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~------------V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~   69 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGE------------VAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKG   69 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--------------EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTS
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCC------------cceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcC
Confidence            56899999999999999999999986            6777777778899999999999999993   33   345566


Q ss_pred             ceEEEc
Q 013837          249 VAVRVR  254 (435)
Q Consensus       249 ~~l~v~  254 (435)
                      ..+.+.
T Consensus        70 ~~~~~~   75 (105)
T PF08777_consen   70 KEVTLE   75 (105)
T ss_dssp             SSEEEE
T ss_pred             ceEEEE
Confidence            555554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.31  E-value=0.00091  Score=51.09  Aligned_cols=83  Identities=19%  Similarity=0.233  Sum_probs=51.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCC-CCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNS-AGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~-~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....|.|-+.|+. ....|.+.|+.||.|+.... ......+.............|+|.++.+|.+||..||..|.|.-|
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            4567999999998 55778999999998643100 000000000024456789999999999999999999999988644


Q ss_pred             -EEcCC
Q 013837          252 -RVRRP  256 (435)
Q Consensus       252 -~v~~~  256 (435)
                       -|.+.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence             45544

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.15  E-value=0.0018  Score=52.50  Aligned_cols=57  Identities=19%  Similarity=0.361  Sum_probs=45.4

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       309 ~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|.+.|..||.|.-|++.-+        .-+|.|.+-+.|.+|+. |+|.+++|+.|+|.+.++.
T Consensus        51 ~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   51 DELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE----
T ss_pred             HHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCcc
Confidence            367788999999877776654        46899999999999999 8999999999999998655

; PDB: 1UFW_A 2DNR_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=97.10  E-value=0.00039  Score=67.77  Aligned_cols=76  Identities=25%  Similarity=0.287  Sum_probs=62.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee---CCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~-~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~---~g~~l~  367 (435)
                      ...+.|+|.||--..|.-.|+.++.. .|.|+..+|  |+    -+..|||.|.+.++|.+.+.+|||..+   +++.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            44578999999999999999999995 555766633  32    245799999999999999999999977   689999


Q ss_pred             EEEccC
Q 013837          368 VRRATA  373 (435)
Q Consensus       368 V~~a~~  373 (435)
                      |.|+..
T Consensus       516 adf~~~  521 (718)
T KOG2416|consen  516 ADFVRA  521 (718)
T ss_pred             eeecch
Confidence            999843

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.08  E-value=0.00041  Score=60.79  Aligned_cols=73  Identities=21%  Similarity=0.427  Sum_probs=61.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC--------CCcce----EEEEEEcCHHHHHHHHHHhCCce
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT--------GNSKG----YGFCVYQDPAVTDIACAALNGLK  360 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t--------g~~~G----~afV~f~~~~~A~~Al~~l~g~~  360 (435)
                      ....||+++||+......|+++|+.||.|=.|.|.....+        |...+    -|+|+|.+...|..+...|||..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            3457999999999999999999999999998888776444        22222    36799999999999999999999


Q ss_pred             eCCeE
Q 013837          361 MGDKT  365 (435)
Q Consensus       361 ~~g~~  365 (435)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.93  E-value=0.0042  Score=44.92  Aligned_cols=54  Identities=15%  Similarity=0.345  Sum_probs=41.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~  357 (435)
                      ...+|. +|..+...||.++|+.||.| .|..+-+.       -|||.+.+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            345555 99999999999999999997 46666652       69999999999999998774

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.87  E-value=0.0014  Score=59.61  Aligned_cols=75  Identities=25%  Similarity=0.423  Sum_probs=57.2

Q ss_pred             CeEEEcCCCCCCCHHH------HHHHHHHHHHhhcCCCCCCCCceEEEEec---CCCcEE--EEEecCHHHHHHHH-HhC
Q 013837          175 RRVYVGGLPPLANEQA------IATFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFA--FVEMRTVEEASNAM-ALD  242 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~------l~~~f~~~G~i~~~~~~~~~~~v~~~~~~---~~~g~a--fv~f~~~~~a~~a~-~l~  242 (435)
                      .-+||-+||+.+..++      -.++|.+||+|..        ++++.++.   ...+.+  ||+|.+.++|..|+ +.+
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~K--------IvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vD  186 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKK--------IVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVD  186 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeE--------EEecccccccccccccceEEEEecchHHHHHHHHHhc
Confidence            3589999999876655      2479999999754        24444442   112334  99999999999999 699


Q ss_pred             CceecCceEEEcCCC
Q 013837          243 GIIFEGVAVRVRRPT  257 (435)
Q Consensus       243 ~~~~~g~~l~v~~~~  257 (435)
                      |..++|+-|+..|..
T Consensus       187 gs~~DGr~lkatYGT  201 (480)
T COG5175         187 GSLLDGRVLKATYGT  201 (480)
T ss_pred             cccccCceEeeecCc
Confidence            999999999998754

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.84  E-value=0.0053  Score=58.60  Aligned_cols=77  Identities=17%  Similarity=0.173  Sum_probs=64.8

Q ss_pred             hcccCCeEEEcCCCCCC-CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~-t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      .....+.|-+.-.|+.. |-++|...|.+||.            |.++.+..+.-.|.|+|.+..+|-.|....+..|++
T Consensus       368 ~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~------------i~n~qv~~~~~~a~vTF~t~aeag~a~~s~~avlnn  435 (526)
T KOG2135|consen  368 AVVDHSPLALEKSPFGLNTIADLNPHFAQFGE------------IENIQVDYSSLHAVVTFKTRAEAGEAYASHGAVLNN  435 (526)
T ss_pred             hhcccchhhhhccCCCCchHhhhhhhhhhcCc------------cccccccCchhhheeeeeccccccchhccccceecC
Confidence            34566778888888876 67999999999998            556666666778999999999998888899999999


Q ss_pred             ceEEEcCCCC
Q 013837          249 VAVRVRRPTD  258 (435)
Q Consensus       249 ~~l~v~~~~~  258 (435)
                      +.|+|.|.++
T Consensus       436 r~iKl~whnp  445 (526)
T KOG2135|consen  436 RFIKLFWHNP  445 (526)
T ss_pred             ceeEEEEecC
Confidence            9999999765

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.81  E-value=0.0065  Score=58.02  Aligned_cols=71  Identities=13%  Similarity=0.201  Sum_probs=57.1

Q ss_pred             EEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          297 VFVGGLPYYF-TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       297 l~V~nLp~~~-te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      |-+.-.|... |-++|...|.+||.|..|.|-...+      -|.|.|.+..+|-.|.. .++..|+++.|+|.|-++.
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhc-cccceecCceeEEEEecCC
Confidence            4444455443 6689999999999999988755422      58999999999977776 6999999999999998873

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.78  E-value=0.00022  Score=72.82  Aligned_cols=80  Identities=19%  Similarity=0.298  Sum_probs=67.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ..+.+||++||+..+++.+|+..|..||.|..|.|...+. +.---||||.|.+...+..|...+.+..|....+++.+.
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            3457899999999999999999999999999999877643 333348999999999999999999999887667777776


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      .
T Consensus       449 ~  449 (975)
T KOG0112|consen  449 Q  449 (975)
T ss_pred             c
Confidence            4

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.68  E-value=0.018  Score=56.08  Aligned_cols=70  Identities=11%  Similarity=0.132  Sum_probs=53.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh--cCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 013837          294 PDRVFVGGLPYYFTETQIKELLES--FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVR  369 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~--~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~V~  369 (435)
                      .|.|+|+-||..+-+|+|+.+|+.  +-++.+|.+..+.       -=||.|++..+|++|.+.|.-  ..|.|+.|...
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            356789999999999999999985  6667777776542       148999999999999987742  35666666544


Q ss_pred             E
Q 013837          370 R  370 (435)
Q Consensus       370 ~  370 (435)
                      .
T Consensus       248 I  248 (684)
T KOG2591|consen  248 I  248 (684)
T ss_pred             h
Confidence            3

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.64  E-value=0.0011  Score=62.30  Aligned_cols=72  Identities=24%  Similarity=0.206  Sum_probs=57.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-------CcEEEEEecCHHHHHHHHHhC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-------KKFAFVEMRTVEEASNAMALD  242 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-------~g~afv~f~~~~~a~~a~~l~  242 (435)
                      +-.+++|.+.|||.+-..+.|.++|..+|.|..+-++.|+.+-.++.-...       +-+|+|+|...+.|.+|.++.
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~  306 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELL  306 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhh
Confidence            357899999999999888999999999999877666666544444433222       579999999999999999744

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.39  E-value=0.025  Score=38.83  Aligned_cols=54  Identities=22%  Similarity=0.408  Sum_probs=44.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESF----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  356 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~----G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l  356 (435)
                      ...|+|+|+. +++.+||+.+|..|    + ...|.++-|.       -|=|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~-~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEG-PFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCC-CceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            4579999996 47888999999999    5 4578888874       4779999999999999865

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.28  E-value=0.0025  Score=62.35  Aligned_cols=75  Identities=13%  Similarity=0.165  Sum_probs=61.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee---c
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF---E  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~---~  247 (435)
                      ..+..|+|.||-.-+|.-+|+.++..-|.+           |....+.+-+..|||.|.+.++|.+.. +|+|..|   +
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~-----------Vee~WmDkIKShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGN-----------VEEFWMDKIKSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCc-----------hHHHHHHHhhcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            567889999999999999999999966543           334455666789999999999999999 6999988   4


Q ss_pred             CceEEEcCCC
Q 013837          248 GVAVRVRRPT  257 (435)
Q Consensus       248 g~~l~v~~~~  257 (435)
                      ++.|.+.|..
T Consensus       511 PK~L~adf~~  520 (718)
T KOG2416|consen  511 PKHLIADFVR  520 (718)
T ss_pred             CceeEeeecc
Confidence            5778887754

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.98  E-value=0.0044  Score=54.50  Aligned_cols=78  Identities=15%  Similarity=0.117  Sum_probs=52.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEE--EEecCCC----cEEEEEecCHHHHHHHH-HhCCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN--VYINHEK----KFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~--~~~~~~~----g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      ..-.||+++||+.+...-|+++|..||.|=.+++.........  ..-+.+.    .-|+|+|.+...|..+. .||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            4457999999999999999999999998621110000000000  0001111    24689999999999988 699999


Q ss_pred             ecCce
Q 013837          246 FEGVA  250 (435)
Q Consensus       246 ~~g~~  250 (435)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99976

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=95.93  E-value=0.0025  Score=64.84  Aligned_cols=75  Identities=13%  Similarity=0.148  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee--CCeEEEEEEccC
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVRRATA  373 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~V~~a~~  373 (435)
                      +..+.|.+...+-..|..+|.+||.|.+++..++-      ..|.|+|...+.|..|+++|+|..+  -|-+.+|.+|+.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            44566667777888999999999999999988873      3799999999999999999999976  588999999987


Q ss_pred             CCC
Q 013837          374 SSG  376 (435)
Q Consensus       374 ~~~  376 (435)
                      .+.
T Consensus       374 ~~~  376 (1007)
T KOG4574|consen  374 LPM  376 (1007)
T ss_pred             ccc
Confidence            664

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.88  E-value=0.0026  Score=58.84  Aligned_cols=81  Identities=14%  Similarity=0.143  Sum_probs=62.1

Q ss_pred             cCCeEE-EcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          173 HARRVY-VGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~-V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...+++ |++|++.+++++|+.+|..+|.|...      .......++..+|||||.|.....+..++......+.++++
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~------r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSV------RLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPL  256 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceee------ccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCccc
Confidence            344555 99999999999999999999886431      11122234567899999999999999999557788999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.+....
T Consensus       257 ~~~~~~~~  264 (285)
T KOG4210|consen  257 RLEEDEPR  264 (285)
T ss_pred             ccccCCCC
Confidence            99876543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=95.87  E-value=0.01  Score=54.42  Aligned_cols=78  Identities=15%  Similarity=0.107  Sum_probs=57.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~l  251 (435)
                      .--++||+||-|.+|++||.+.+...|-. .+   ...+-..+-..+.+||||+|...+....++.|+ |...+|+|..-
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~-~~---~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P  154 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLA-QF---ADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSP  154 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHH-HH---hhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCC
Confidence            34579999999999999999998877642 00   000012222346789999999999999999995 88889998765


Q ss_pred             EEc
Q 013837          252 RVR  254 (435)
Q Consensus       252 ~v~  254 (435)
                      .|-
T Consensus       155 ~V~  157 (498)
T KOG4849|consen  155 TVL  157 (498)
T ss_pred             eee
Confidence            554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.85  E-value=0.014  Score=47.38  Aligned_cols=53  Identities=26%  Similarity=0.333  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcCC
Q 013837          190 AIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRP  256 (435)
Q Consensus       190 ~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~~  256 (435)
                      +|.+.|..||++            +-+++..  +.-+|+|.+.+.|.+|+.++|.+++|+.|+|..-
T Consensus        52 ~ll~~~~~~Gev------------vLvRfv~--~~mwVTF~dg~sALaals~dg~~v~g~~l~i~LK  104 (146)
T PF08952_consen   52 ELLQKFAQYGEV------------VLVRFVG--DTMWVTFRDGQSALAALSLDGIQVNGRTLKIRLK  104 (146)
T ss_dssp             HHHHHHHCCS-E------------CEEEEET--TCEEEEESSCHHHHHHHHGCCSEETTEEEEEEE-
T ss_pred             HHHHHHHhCCce------------EEEEEeC--CeEEEEECccHHHHHHHccCCcEECCEEEEEEeC
Confidence            555666667763            3334332  5789999999999999999999999999999853

; PDB: 1UFW_A 2DNR_A.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=95.80  E-value=0.015  Score=56.42  Aligned_cols=79  Identities=15%  Similarity=0.175  Sum_probs=57.5

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHH-HHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceec-
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFS-QVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE-  247 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~-~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~-  247 (435)
                      .....+|||||+||.-++.++|..+|+ -||.|+-.      .+-+|.+.+..+|-|=|+|.+...-.+||..--.+|. 
T Consensus       366 ~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~ya------GIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h  439 (520)
T KOG0129|consen  366 PIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYV------GIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDH  439 (520)
T ss_pred             ccCccceEEecCCCCcchHHHHHHHHHHhcCceEEE------EeccCcccCCCCCcceeeecccHHHHHHHhhheEEEec
Confidence            346789999999999999999999999 78875431      1112224455789999999999999999953333332 


Q ss_pred             ---CceEEEc
Q 013837          248 ---GVAVRVR  254 (435)
Q Consensus       248 ---g~~l~v~  254 (435)
                         .+.|.|+
T Consensus       440 ~d~~KRVEIk  449 (520)
T KOG0129|consen  440 TDIDKRVEIK  449 (520)
T ss_pred             cccceeeeec
Confidence               2456665

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=95.73  E-value=0.017  Score=49.50  Aligned_cols=82  Identities=13%  Similarity=0.082  Sum_probs=51.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHh-cCCe---eEEEEeecCC-CCC-cceEEEEEEcCHHHHHHHHHHhCCceeC---C-
Q 013837          294 PDRVFVGGLPYYFTETQIKELLES-FGTL---HGFDLVKDRD-TGN-SKGYGFCVYQDPAVTDIACAALNGLKMG---D-  363 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~-~G~v---~~v~i~~~~~-tg~-~~G~afV~f~~~~~A~~Al~~l~g~~~~---g-  363 (435)
                      ..+|.|++||+.+|++++.+.+.. ++.-   ..+.-..... ... .-.-|||.|.+.+++...+..++|+.|-   | 
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            458999999999999999887776 5554   2232112111 111 2245999999999999999999998873   2 


Q ss_pred             -eEEEEEEccCCC
Q 013837          364 -KTLTVRRATASS  375 (435)
Q Consensus       364 -~~l~V~~a~~~~  375 (435)
                       ....|+||--+.
T Consensus        87 ~~~~~VE~Apyqk   99 (176)
T PF03467_consen   87 EYPAVVEFAPYQK   99 (176)
T ss_dssp             EEEEEEEE-SS--
T ss_pred             CcceeEEEcchhc
Confidence             467888886543

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=95.68  E-value=0.098  Score=47.33  Aligned_cols=73  Identities=18%  Similarity=0.186  Sum_probs=56.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-EEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~V~~a~  372 (435)
                      ...|.|-++|.. .-..|..+|++||.|++....   .+|   .+-+|.|.+.-+|.+||. .||..|+|. .|-|..+.
T Consensus       197 D~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~---~ng---NwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  197 DTWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTP---SNG---NWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             cceEEEeccCcc-chhHHHHHHHhhCeeeeeecC---CCC---ceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecC
Confidence            457888898876 345688999999999665443   223   388999999999999999 699999875 46677765


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      .+
T Consensus       269 Dk  270 (350)
T KOG4285|consen  269 DK  270 (350)
T ss_pred             CH
Confidence            54

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.59  E-value=0.0043  Score=56.97  Aligned_cols=80  Identities=19%  Similarity=0.347  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCC----CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          295 DRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~---~~F~~~G~v~~v~i~~~~~----tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .-+||-+|+..+..+.+.   +.|.+||.|..|.+..+..    .+-.- -+||.|...++|..||...+|+.+.|+.|+
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~-s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTC-SVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCC-cccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            357888888776555443   5788999999988887652    11111 289999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      ..|.+.+-
T Consensus       157 a~~gttky  164 (327)
T KOG2068|consen  157 ASLGTTKY  164 (327)
T ss_pred             HhhCCCcc
Confidence            98886654

>KOG2548 consensus SWAP mRNA splicing regulator [RNA processing and modification]

Probab=95.56  E-value=0.0048  Score=59.45  Aligned_cols=15  Identities=7%  Similarity=-0.274  Sum_probs=6.0

Q ss_pred             CCCCCCCHHHHHHHH
Q 013837          181 GLPPLANEQAIATFF  195 (435)
Q Consensus       181 nlp~~~t~~~l~~~f  195 (435)
                      |--+..|...+...|
T Consensus       556 ~~r~klt~~~~lk~r  570 (653)
T KOG2548|consen  556 NSRPKLTFFECLKSR  570 (653)
T ss_pred             CCCCcccHHHHHHHH
Confidence            333344544433333

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.42  E-value=0.2  Score=39.06  Aligned_cols=68  Identities=12%  Similarity=0.177  Sum_probs=52.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~-v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ...+++...|..++-++|..+.+.+-. |..++|+++.  ..++-.+.++|.+.+.|..-...+||..|+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            344556666777777788777776654 7788998873  2356679999999999999999999998853

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.31  E-value=0.024  Score=55.43  Aligned_cols=79  Identities=20%  Similarity=0.274  Sum_probs=55.3

Q ss_pred             ccCCeEEEcCCCCCC--C----HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          172 RHARRVYVGGLPPLA--N----EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~--t----~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      .....|+|.|+|---  .    ..-|.++|+++|+++..+..      . ..-+..+||.|++|.+..+|..|+ .|||+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P------~-~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~  128 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYP------I-DEEGGTKGYLFVEYASMRDAKKAVKSLNGK  128 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeec------c-CccCCeeeEEEEEecChhhHHHHHHhcccc
Confidence            455689999998632  2    24466789999987553210      0 112447899999999999999999 69999


Q ss_pred             eec-CceEEEcCCC
Q 013837          245 IFE-GVAVRVRRPT  257 (435)
Q Consensus       245 ~~~-g~~l~v~~~~  257 (435)
                      .|. .+...|..-+
T Consensus       129 ~ldknHtf~v~~f~  142 (698)
T KOG2314|consen  129 RLDKNHTFFVRLFK  142 (698)
T ss_pred             eecccceEEeehhh
Confidence            875 4566665433

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.28  E-value=0.058  Score=46.36  Aligned_cols=62  Identities=19%  Similarity=0.258  Sum_probs=45.8

Q ss_pred             CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC--CceeCCeEEEEEEccCC
Q 013837          307 TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTVRRATAS  374 (435)
Q Consensus       307 te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~V~~a~~~  374 (435)
                      ..+.|+++|..|+.+..+.+++.      -+=..|.|.+.+.|..|...|+  +..|.|..|+|.|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            45789999999999877766654      2358899999999999999999  99999999999999544

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG3263 consensus Nucleic acid binding protein [General function prediction only]

Probab=95.21  E-value=0.0049  Score=50.41  Aligned_cols=11  Identities=0%  Similarity=-0.070  Sum_probs=5.3

Q ss_pred             HHHHHHHHHHH
Q 013837          189 QAIATFFSQVM  199 (435)
Q Consensus       189 ~~l~~~f~~~G  199 (435)
                      +++.+++.-.|
T Consensus       141 eEeiEMmk~MG  151 (196)
T KOG3263|consen  141 EEEIEMMKIMG  151 (196)
T ss_pred             HHHHHHHHHhC
Confidence            33455555444

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.12  E-value=0.13  Score=41.24  Aligned_cols=73  Identities=14%  Similarity=0.174  Sum_probs=53.9

Q ss_pred             CCCCCeEEEcCCCCCC----CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          291 AEGPDRVFVGGLPYYF----TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~----te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ..+..+|.|+=|..++    +...|...++.||+|.+|.+.-       +--|.|.|.+..+|-+|+.+++. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            3455688887665554    3345666788999999987643       23699999999999999999876 5567777


Q ss_pred             EEEEc
Q 013837          367 TVRRA  371 (435)
Q Consensus       367 ~V~~a  371 (435)
                      .+.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            77764

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.09  E-value=0.017  Score=51.00  Aligned_cols=63  Identities=17%  Similarity=0.189  Sum_probs=45.1

Q ss_pred             HHHHHHHH-HHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCCC
Q 013837          189 QAIATFFS-QVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD  258 (435)
Q Consensus       189 ~~l~~~f~-~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~~  258 (435)
                      ++|...|. +||+|...+       |.+..-..-.|-+||.|...++|.+|+ .||+--+.|++|...++..
T Consensus        83 Ed~f~E~~~kygEiee~~-------Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pv  147 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELN-------VCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPV  147 (260)
T ss_pred             HHHHHHHHHHhhhhhhhh-------hhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCc
Confidence            44555555 788875432       122112223689999999999999999 6999999999999887543

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=94.74  E-value=0.2  Score=35.06  Aligned_cols=55  Identities=18%  Similarity=0.265  Sum_probs=44.9

Q ss_pred             CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          305 YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       305 ~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      .++-++|+..+..|+-.   .|..++     .|| ||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            47889999999999763   344553     455 89999999999999999999998887654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.30  E-value=0.048  Score=54.59  Aligned_cols=69  Identities=14%  Similarity=0.140  Sum_probs=56.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.-+|||+|+...+..+-++.++..+|.|..+.            ..   -|+|++|..+..+..|+ .++...++|..
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~k------------r~---~fgf~~f~~~~~~~ra~r~~t~~~~~~~k  102 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWK------------RD---KFGFCEFLKHIGDLRASRLLTELNIDDQK  102 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhh------------hh---hhcccchhhHHHHHHHHHHhcccCCCcch
Confidence            4566899999999999999999999999864421            11   19999999999999999 57778888888


Q ss_pred             EEEcC
Q 013837          251 VRVRR  255 (435)
Q Consensus       251 l~v~~  255 (435)
                      +.+..
T Consensus       103 l~~~~  107 (668)
T KOG2253|consen  103 LIENV  107 (668)
T ss_pred             hhccc
Confidence            77753

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.16  E-value=0.3  Score=44.30  Aligned_cols=73  Identities=23%  Similarity=0.327  Sum_probs=58.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce-EE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-VR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~-l~  252 (435)
                      ..-|.|-++|+..+ .-|..+|..||.            |++..+..+..+-+|.|.+.-+|.+||..||..|+|.. |-
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~------------Vvkhv~~~ngNwMhirYssr~~A~KALskng~ii~g~vmiG  263 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGE------------VVKHVTPSNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIG  263 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCe------------eeeeecCCCCceEEEEecchhHHHHhhhhcCeeeccceEEe
Confidence            56788889988765 457889999998            55566667778999999999999999999999998854 56


Q ss_pred             EcCCCCC
Q 013837          253 VRRPTDY  259 (435)
Q Consensus       253 v~~~~~~  259 (435)
                      |..+.+.
T Consensus       264 VkpCtDk  270 (350)
T KOG4285|consen  264 VKPCTDK  270 (350)
T ss_pred             eeecCCH
Confidence            7665544

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=93.30  E-value=0.46  Score=34.21  Aligned_cols=59  Identities=24%  Similarity=0.318  Sum_probs=35.4

Q ss_pred             CCCCHHHHHHHHHhcCCe-----eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          304 YYFTETQIKELLESFGTL-----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       304 ~~~te~~l~~~F~~~G~v-----~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ..++..+|..++...+.|     -.|.|...        |+||+-... .|..++..|++..+.|+.|+|+.|
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            357788888888876554     34555443        899988654 788899999999999999999875

; PDB: 2G0C_A 3MOJ_B.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=92.80  E-value=0.29  Score=44.15  Aligned_cols=62  Identities=23%  Similarity=0.164  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC---CCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCC
Q 013837          188 EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH---EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       188 ~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~---~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~  257 (435)
                      ++++.+-..+||.|..+        |+...-+.   ..--.||+|...++|.+|+ .|||..|+|+.+...+-+
T Consensus       300 ede~keEceKyg~V~~v--------iifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNV--------IIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeE--------EEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            46778888999987432        22222111   1235799999999999999 799999999998877643

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=92.69  E-value=0.13  Score=51.65  Aligned_cols=70  Identities=26%  Similarity=0.410  Sum_probs=59.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+..++||+|+-..+..+-++.+...+|.|..+....         |+|++|..+..+..|+..|+-..++|..+.+.-
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            3456899999999999999999999999986554433         899999999999999999999999888776665

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.38  E-value=0.59  Score=44.92  Aligned_cols=68  Identities=18%  Similarity=0.293  Sum_probs=58.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~-v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ...|+|-.+|..+|-.||..|+..|-. |..|+|++|..  ..+=.++|.|.+.++|....+.+||..|+.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            678999999999999999999998765 89999999743  234468999999999999999999998853

>KOG2891 consensus Surface glycoprotein [General function prediction only]

Probab=92.34  E-value=0.15  Score=45.43  Aligned_cols=80  Identities=23%  Similarity=0.448  Sum_probs=54.2

Q ss_pred             CCCeEEEcCCCCC------------CCHHHHHHHHHhcCCeeEEEEeec-C----CCCCc-----ceE---------EEE
Q 013837          293 GPDRVFVGGLPYY------------FTETQIKELLESFGTLHGFDLVKD-R----DTGNS-----KGY---------GFC  341 (435)
Q Consensus       293 ~~~~l~V~nLp~~------------~te~~l~~~F~~~G~v~~v~i~~~-~----~tg~~-----~G~---------afV  341 (435)
                      .+.||++.+||..            .++.-|...|+.||.|..|.|+.- +    .+|+.     .||         |||
T Consensus       148 rpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayv  227 (445)
T KOG2891|consen  148 RPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYV  227 (445)
T ss_pred             CCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHH
Confidence            3457888777754            356789999999999988887642 1    23443     233         457


Q ss_pred             EEcCHHHHHHHHHHhCCcee----CC----eEEEEEEcc
Q 013837          342 VYQDPAVTDIACAALNGLKM----GD----KTLTVRRAT  372 (435)
Q Consensus       342 ~f~~~~~A~~Al~~l~g~~~----~g----~~l~V~~a~  372 (435)
                      +|.....-..|+.+|.|..+    .|    -.|+|.|..
T Consensus       228 qfmeykgfa~amdalr~~k~akk~d~~ffqanvkvdfdr  266 (445)
T KOG2891|consen  228 QFMEYKGFAQAMDALRGMKLAKKGDDGFFQANVKVDFDR  266 (445)
T ss_pred             HHHHHHhHHHHHHHHhcchHHhhcCCcccccccccccch
Confidence            77777777888888888765    22    356676653

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=91.59  E-value=1.3  Score=30.56  Aligned_cols=55  Identities=16%  Similarity=0.251  Sum_probs=38.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~  239 (435)
                      ...|+|.|+ .+++.++|+.+|..|...         .....+... +-..|-|.|.+.+.|.+||
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~---------~~~~~IEWI-dDtScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDE---------EGPFRIEWI-DDTSCNVVFKDEETAARAL   59 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhccc---------CCCceEEEe-cCCcEEEEECCHHHHHHHH
Confidence            347999999 457788999999999221         012222221 2346789999999999998

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=90.24  E-value=1.1  Score=39.94  Aligned_cols=74  Identities=18%  Similarity=0.091  Sum_probs=55.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h--CC--ceecCc
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L--DG--IIFEGV  249 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l--~~--~~~~g~  249 (435)
                      ..|+|.||...+..+.|...|..||.|-..       +++...-+...+-++|+|...-.|.+|+. .  .+  .+..+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~a-------v~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~  104 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERA-------VAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGR  104 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchh-------eeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCC
Confidence            579999999999999999999999987442       23333345667889999999999999984 2  22  334556


Q ss_pred             eEEEcC
Q 013837          250 AVRVRR  255 (435)
Q Consensus       250 ~l~v~~  255 (435)
                      +..|..
T Consensus       105 p~~VeP  110 (275)
T KOG0115|consen  105 PVGVEP  110 (275)
T ss_pred             ccCCCh
Confidence            666653

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=89.64  E-value=0.13  Score=44.08  Aligned_cols=67  Identities=16%  Similarity=0.223  Sum_probs=42.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHH-HHHhhcCCCCCCCCceEEEE--ecC------CCcEEEEEecCHHHHHHHH-HhC
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVY--INH------EKKFAFVEMRTVEEASNAM-ALD  242 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~~v~~~~--~~~------~~g~afv~f~~~~~a~~a~-~l~  242 (435)
                      ...+|.|++||+++|++++.+.+.. ++....         ...+.  .+.      .-.-|||.|.+.+++...+ .++
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~---------w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~   76 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWD---------WYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFD   76 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE------------EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCT
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccc---------eEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcC
Confidence            4568999999999999999986665 332100         11111  111      1258999999999999888 599


Q ss_pred             CceecC
Q 013837          243 GIIFEG  248 (435)
Q Consensus       243 ~~~~~g  248 (435)
                      |+.|.+
T Consensus        77 g~~F~D   82 (176)
T PF03467_consen   77 GHVFVD   82 (176)
T ss_dssp             TEEEE-
T ss_pred             CcEEEC
Confidence            988754

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=88.56  E-value=2.4  Score=40.92  Aligned_cols=67  Identities=12%  Similarity=0.271  Sum_probs=52.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      +..|+|-.+|..+|..||..|...+-..+.        .|.-+..+ .++-.+.|.|.+.++|..+. ++||..|..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~--------~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQIS--------DIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhh--------eeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            778999999999999999999998865422        13333333 23457889999999999999 699998875

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=88.27  E-value=2.1  Score=29.96  Aligned_cols=54  Identities=11%  Similarity=0.123  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          185 LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       185 ~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      .++-++|+..+..|+-             ..+... ..| -||.|.+..+|++|. ..++..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~-------------~~I~~d-~tG-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW-------------DRIRDD-RTG-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc-------------ceEEec-CCE-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            4678999999999852             222221 234 489999999999999 58888888777665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=87.56  E-value=0.95  Score=33.01  Aligned_cols=51  Identities=20%  Similarity=0.230  Sum_probs=36.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA  240 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~  240 (435)
                      ...+|. +|......||.++|..||.|            .-..+  +-..|||.....+.|..|+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I------------~VsWi--~dTSAfV~l~~r~~~~~v~~   60 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQI------------YVSWI--NDTSAFVALHNRDQAKVVMN   60 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCE------------EEEEE--CTTEEEEEECCCHHHHHHHH
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcE------------EEEEE--cCCcEEEEeecHHHHHHHHH
Confidence            345555 99999999999999999863            22333  34689999999999999983

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=87.39  E-value=0.57  Score=34.81  Aligned_cols=77  Identities=17%  Similarity=0.182  Sum_probs=47.3

Q ss_pred             EEEEecCHHHHHHHHHhCCc--eecCceEEEc--CCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEc
Q 013837          225 AFVEMRTVEEASNAMALDGI--IFEGVAVRVR--RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVG  300 (435)
Q Consensus       225 afv~f~~~~~a~~a~~l~~~--~~~g~~l~v~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~  300 (435)
                      |+|+|.+..-|...+.+..+  .+++..+.|.  ..........                      ........++|.|.
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~----------------------qv~~~vs~rtVlvs   58 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKF----------------------QVFSGVSKRTVLVS   58 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEE----------------------EEEEcccCCEEEEe
Confidence            68999999999999965444  4556555553  1111100000                      00012345789999


Q ss_pred             CCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          301 GLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       301 nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                      |||....+++|++.       +.|.+.+..
T Consensus        59 gip~~l~ee~l~D~-------LeIhFqK~s   81 (88)
T PF07292_consen   59 GIPDVLDEEELRDK-------LEIHFQKPS   81 (88)
T ss_pred             CCCCCCChhhheee-------EEEEEecCC
Confidence            99999999999874       445555543

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.20  E-value=2.7  Score=41.88  Aligned_cols=81  Identities=15%  Similarity=0.246  Sum_probs=62.4

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhc----CCeeEEEEeecC----------CCCC---------------------
Q 013837          291 AEGPDRVFVGGLPYY-FTETQIKELLESF----GTLHGFDLVKDR----------DTGN---------------------  334 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~----G~v~~v~i~~~~----------~tg~---------------------  334 (435)
                      ...++.|-|-||.|. +..+||.-+|+.|    |.|++|.|....          .+|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456778999999986 7889999998876    578999887531          0121                     


Q ss_pred             ----------------cceEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEEEEc
Q 013837          335 ----------------SKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTVRRA  371 (435)
Q Consensus       335 ----------------~~G~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~V~~a  371 (435)
                                      -.=||.|+|.+++.|.+....+.|..|.  +..|-+.|.
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRFI  305 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRFI  305 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeeec
Confidence                            0127999999999999999999999996  566666664

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=84.65  E-value=1.9  Score=37.15  Aligned_cols=59  Identities=22%  Similarity=0.158  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC--CceecCceEEEcCCCC
Q 013837          188 EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEGVAVRVRRPTD  258 (435)
Q Consensus       188 ~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g~~l~v~~~~~  258 (435)
                      .+.|+++|..|+.            ++....-.+-+-..|.|.+.+.|..|. .|+  +..+.|..++|.++..
T Consensus         9 ~~~l~~l~~~~~~------------~~~~~~L~sFrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    9 LAELEELFSTYDP------------PVQFSPLKSFRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             HHHHHHHHHTT-S------------S-EEEEETTTTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             HHHHHHHHHhcCC------------ceEEEEcCCCCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            4778888888865            445555567788999999999999999 588  8999999999988743

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=84.48  E-value=2.9  Score=37.77  Aligned_cols=48  Identities=4%  Similarity=0.013  Sum_probs=39.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHH
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE  233 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~  233 (435)
                      ..|+|+||+.++--.||+..+...|.+           -..+......|-||+.|.+..
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~-----------pm~iswkg~~~k~flh~~~~~  378 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECT-----------PMSISWKGHFGKCFLHFGNRK  378 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCC-----------ceeEeeecCCcceeEecCCcc
Confidence            459999999999999999999988652           556667778899999998754

>KOG1882 consensus Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms]

Probab=84.07  E-value=0.9  Score=39.95  Aligned_cols=12  Identities=25%  Similarity=0.349  Sum_probs=4.4

Q ss_pred             CCCCCccccCCC
Q 013837           22 VSGRSRTGERGR   33 (435)
Q Consensus        22 ~~~r~~~r~r~r   33 (435)
                      +....+++.+++
T Consensus        15 sp~~~Rsr~~s~   26 (293)
T KOG1882|consen   15 SPRGNRSRGRSR   26 (293)
T ss_pred             Cccccccchhhh
Confidence            333333333333

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=83.73  E-value=1.5  Score=43.39  Aligned_cols=70  Identities=14%  Similarity=0.266  Sum_probs=50.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h--CCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L--DGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l--~~~~~~g  248 (435)
                      ..-|.|+|+-||..+-+++|+.||..-  -+        -.++++.+..+.+ .||+|.+..+|+.|.. |  .-.+|.|
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~e--nc--------Pk~iscefa~N~n-WyITfesd~DAQqAykylreevk~fqg  241 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGE--NC--------PKVISCEFAHNDN-WYITFESDTDAQQAYKYLREEVKTFQG  241 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccC--CC--------CCceeeeeeecCc-eEEEeecchhHHHHHHHHHHHHHhhcC
Confidence            455778999999999999999999842  00        1367777665544 6999999999999973 2  2245666


Q ss_pred             ceEE
Q 013837          249 VAVR  252 (435)
Q Consensus       249 ~~l~  252 (435)
                      ++|.
T Consensus       242 KpIm  245 (684)
T KOG2591|consen  242 KPIM  245 (684)
T ss_pred             cchh
Confidence            6543

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=82.89  E-value=5.3  Score=31.18  Aligned_cols=66  Identities=12%  Similarity=0.163  Sum_probs=40.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ..+.+...|..++-++|..+...+-..+.        .+..++.+. ++-.+.++|.+.+.|..+. .+||..|+.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~--------~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIE--------HIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEE--------EEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            33444444455566666655555533211        122223232 4457889999999999999 699988864

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=81.61  E-value=6.8  Score=31.80  Aligned_cols=73  Identities=14%  Similarity=0.082  Sum_probs=49.2

Q ss_pred             ccCCeEEEcCCCCCC-CHHH---HHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          172 RHARRVYVGGLPPLA-NEQA---IATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~-t~~~---l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .+-.||.|+=|..++ ..+|   |...+..||.|            ..+ +...+..|.|.|.+..+|-.|+ ++.. ..
T Consensus        84 pPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI------------~SV-T~cGrqsavVvF~d~~SAC~Av~Af~s-~~  149 (166)
T PF15023_consen   84 PPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPI------------QSV-TLCGRQSAVVVFKDITSACKAVSAFQS-RA  149 (166)
T ss_pred             CCceeEEeehhhhcCChHHHHHHHHHHHHhcCCc------------cee-eecCCceEEEEehhhHHHHHHHHhhcC-CC
Confidence            445689998776665 2334   44556677764            222 3346789999999999999999 4554 56


Q ss_pred             cCceEEEcCCCC
Q 013837          247 EGVAVRVRRPTD  258 (435)
Q Consensus       247 ~g~~l~v~~~~~  258 (435)
                      .|..+...|-..
T Consensus       150 pgtm~qCsWqqr  161 (166)
T PF15023_consen  150 PGTMFQCSWQQR  161 (166)
T ss_pred             CCceEEeecccc
Confidence            667777766543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	435
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		2e-44
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		1e-42
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		1e-42
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		1e-19
1u2f_A	90	Solution Structure Of The First Rna-Binding Domain		5e-19
2hzc_A	87	Crystal Structure Of The N-terminal Rrm Of The U2af		8e-17
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-12
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		5e-10
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-09
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-09
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		5e-09
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-09
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		6e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		9e-09
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		5e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-07
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		7e-07
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		8e-07
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-06
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		2e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		5e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		8e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		8e-06
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		1e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-05
2khc_A	118	Bruno Rrm3+ Length = 118		1e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		1e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		2e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-05
3smz_A	284	Human Raver1 Rrm1-3 Domains (Residues 39-320) Lengt		4e-05
3vf0_B	285	Raver1 In Complex With Metavinculin L954 Deletion M		4e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		5e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-05
3h2u_B	283	Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Comple		5e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		6e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-05
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		1e-04
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		1e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		3e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		4e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		5e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		5e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		7e-04

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score =  176 bits (447), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 94/200 (47%), Positives = 129/200 (64%), Gaps = 10/200 (5%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P       PG  S N ++   G+ S  +   + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL------PGM-SENPSVYVPGVVSTVV--PDS 113
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 354 AALNGLKMGDKTLTVRRATA 373
           A LNG+++GDK L V+RA+ 
Sbjct: 174 AGLNGMQLGDKKLLVQRASV 193

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score =  170 bits (431), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 93
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score =  170 bits (431), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 91/199 (45%), Positives = 121/199 (60%), Gaps = 30/199 (15%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY           QP P                  G
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRPHDY-----------QPLP------------------G 95
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 96  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 156 AGLNGMQLGDKKLLVQRAS 174

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 94.4 bits (233), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/80 (56%), Positives = 57/80 (71%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 356 LNGLKMGDKTLTVRRATASS 375
           LNG+++GDK L V+RA+  +
Sbjct: 63  LNGMQLGDKKLLVQRASVGA 82

>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of Hu2af65 Length = 90

Iteration: 1
 Score = 92.4 bits (228), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 43/88 (48%), Positives = 62/88 (70%), Gaps = 1/88 (1%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 59
Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNP 261
           E + AMA DGIIF+G ++++RRP DY P
Sbjct: 60  ETTQAMAFDGIIFQGQSLKIRRPHDYQP 87

>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large Subunit Length = 87

Iteration: 1
 Score = 84.7 bits (208), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 40/83 (48%), Positives = 59/83 (71%), Gaps = 1/83 (1%)
Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 234 EASNAMALDGIIFEGVAVRVRRP 256
           E + AMA DGIIF+G ++++RRP
Sbjct: 65  ETTQAMAFDGIIFQGQSLKIRRP 87

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 69.7 bits (169), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 38/88 (43%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   L
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQES 384
           NG +   + L V    A+S ++K E +S
Sbjct: 71  NGREFSGRALRV--DNAASEKNKEELKS 96

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 34/80 (42%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGLK+  KT+ V  A  SS 
Sbjct: 67  NGLKLQTKTIKVSYARPSSA 86

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 62.4 bits (150), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 44/83 (53%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ GP R++VG L +  TE  ++ + E FG +    L+ D +TG SKGYGF  + D    
Sbjct: 22  GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 82  KKALEQLNGFELAGRPMKVGHVT 104

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/80 (42%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + K L  S G +    LV+D+ TG S GYGF  Y DP   D A   L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGLK+  KT+ V  A  SS 
Sbjct: 67  NGLKLQTKTIKVSYARPSSA 86

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 53/202 (26%), Positives = 88/202 (43%), Gaps = 33/202 (16%)
Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV----NVYINHEKKFAFVEMRT 231
           RVYVG +     E  I   F+           GP  ++     +V + H K FAFVE   
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPF---------GPIKSIDMSWDSVTMKH-KGFAFVEYEV 79
Query: 232 VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
            E A  A+  ++ ++  G  ++V RP++           GQ  P ++  A          
Sbjct: 80  PEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQPIIDQLA--------EE 121
Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  Y+    + 
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ 181
Query: 351 IACAALNGLKMGDKTLTVRRAT 372
            A +++N   +G + L V +A 
Sbjct: 182 DAVSSMNLFDLGGQYLRVGKAV 203

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVT 83

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 40/69 (57%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 356 LNGLKMGDK 364
            N +  G K
Sbjct: 79  PNPIIDGRK 87

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 91/210 (43%), Gaps = 33/210 (15%)
Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV----NVYINHEKK 223
           Q+A     RVYVG +     E  I   F+           GP  ++     +V + H K 
Sbjct: 7   QRALAIMCRVYVGSIYYELGEDTIRQAFAPF---------GPIKSIDMSWDSVTMKH-KG 56
Query: 224 FAFVEMRTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG 282
           FAFVE    E A  A+  ++ ++  G  ++V RP++           GQ  P ++  A  
Sbjct: 57  FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI----------GQAQPIIDQLA-- 104
Query: 283 LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
                   A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  
Sbjct: 105 ------EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 158
Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+    +  A +++N   +G + L V +A 
Sbjct: 159 YEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 188

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 58.2 bits (139), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 42/80 (52%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 357 NGLKMGDKTLTVRRATASSG 376
           NGL++  KT+ V  A  SS 
Sbjct: 65  NGLRLQTKTIKVSYARPSSA 84

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    A A L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 357 NGLKMGDKTLTVRRATASSGQSK 379
           NG  + +K L V  A A+SG  +
Sbjct: 105 NGFNILNKRLKV--ALAASGHQR 125

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 85/208 (40%), Gaps = 29/208 (13%)
Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFA 225
           Q+A     RVYVG +     E  I   F+    + +I        D   +      K FA
Sbjct: 6   QRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSI--------DXSWDSVTXKHKGFA 57
Query: 226 FVEMRTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           FVE    E A  A+   + +   G  ++V RP++           GQ  P ++  A    
Sbjct: 58  FVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI----------GQAQPIIDQLA---- 103
Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
                 A   +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF  Y+
Sbjct: 104 ----EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRAT 372
               +  A ++ N   +G + L V +A 
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRVGKAV 187

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 353 CAALNGLKMGDKTLTVRRATASS 375
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 42/83 (50%)
Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A
Sbjct: 1   GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 353 CAALNGLKMGDKTLTVRRATASS 375
              LNGL++  KT+ V  A  SS
Sbjct: 61  INTLNGLRLQSKTIKVSYARPSS 83

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 51.6 bits (122), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62
Query: 351 IACAALNGLKMGDKTLTVRRATASSGQS 378
            A   +NG  +  K + V +A   S QS
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQS 90

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 293 GPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           GP R  + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      +
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 351 IACAALNGLKMGDKTLTVRRATAS 374
            A   LNGL++  KT+ V  A  S
Sbjct: 61  RAINTLNGLRLQSKTIKVSYARPS 84

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A L
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 357 NGLKMGDKTLTVRRA 371
           +      +T+ V  A
Sbjct: 63  DNTDFMGRTIRVTEA 77

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 45/80 (56%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 356 LNGLKMGDKTLTVRRATASS 375
           +NG  +  + + V +A  SS
Sbjct: 74  MNGKSVDGRQIRVDQAGKSS 93

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 293 GPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           GP RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  
Sbjct: 1   GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 352 ACAALNGLKMGDKTL 366
           A   LNG ++G + L
Sbjct: 61  AVRNLNGYQLGSRFL 75

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 282 GLASGAIGGA----EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNS 335
           GL   +IG A    EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  S
Sbjct: 7   GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR 369
           K +GF  Y +P     A  ++NG ++G K L V+
Sbjct: 67  KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ 100

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 353 CAALNGLKMGDKTL 366
              LNG ++G + L
Sbjct: 61  VRNLNGYQLGSRFL 74

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 48.5 bits (114), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           P RV ++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A
Sbjct: 3   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 353 CAALNGLKMGDKTL 366
              LNG ++G + L
Sbjct: 63  VRNLNGYQLGSRFL 76

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 4   GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 61
Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQS 378
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 62  ERACRMMNGMKLSGREIDVRIDRNASGPS 90

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
            + L    K +  +RA     Q KT
Sbjct: 65  QHIL--DGKVIDPKRAIPRDEQDKT 87

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 292 EGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           EGP+   +F+  LP  FT+T +      FG +    +  D+ T  SK +GF  + +P   
Sbjct: 36  EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 350 DIACAALNGLKMGDKTLTVR 369
            +A  A+NG ++G K L V+
Sbjct: 96  QVAIKAMNGFQVGTKRLKVQ 115

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 2/89 (2%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   +FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V 
Sbjct: 1   GSSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVA 58
Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQS 378
           + AC  +NG+K+  + + VR    +SG S
Sbjct: 59  ERACRMMNGMKLSGREIDVRIDRNASGPS 87

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/78 (33%), Positives = 40/78 (51%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ +++ L  S G +    L++D+  G+S GYGF  Y      + A   L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 357 NGLKMGDKTLTVRRATAS 374
           NGL++  KT+ V  A  S
Sbjct: 82  NGLRLQSKTIKVSYARPS 99

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 66
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 67  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 106
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 107 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 157
Query: 347 AVTD 350
              D
Sbjct: 158 DSVD 161

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 347 AVTD 350
              D
Sbjct: 157 DSVD 160

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 64
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 65  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 104
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 105 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 155
Query: 347 AVTD 350
              D
Sbjct: 156 DSVD 159

>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320) Length = 284

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 158 LGKPLGPRTLYVHWTDA 174

>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant Length = 285

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 98  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 158 LGKPLGPRTLYVHWTDA 174

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
           +D A  A+NG  + ++ +TV  A
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYA 83

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 58
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 59  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 98
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 99  ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149
Query: 347 AVTD 350
              D
Sbjct: 150 DSVD 153

>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With Human Vinculin Tail Domain Vt Length = 283

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 37/77 (48%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ Q +EL+  FG+L    LV    TG SKGYGF  Y        A + L
Sbjct: 96  LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 357 NGLKMGDKTLTVRRATA 373
            G  +G +TL V    A
Sbjct: 156 LGKPLGPRTLYVHWTDA 172

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 65
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 66  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 105
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 106 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 347 AVTD 350
              D
Sbjct: 157 DSVD 160

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 42/184 (22%), Positives = 73/184 (39%), Gaps = 45/184 (24%)
Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
           R++++GGL     ++++ + F Q  T          D VV    N ++   F FV   TV
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLT--------DCVVMRDPNTKRSRGFGFVTYATV 63
Query: 233 EEASNAM-----ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQ-PSPNLNLAAVGLASG 286
           EE   AM      +DG + E             P  A +    Q P  +L +        
Sbjct: 64  EEVDAAMNARPHKVDGRVVE-------------PKRAVSREDSQRPGAHLTVK------- 103
Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
                    ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D 
Sbjct: 104 ---------KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 154
Query: 347 AVTD 350
              D
Sbjct: 155 DSVD 158

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 353 CAALN----GLKMG 362
            + +N     LK+G
Sbjct: 68  ESQINFHGKKLKLG 81

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/74 (37%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 9   PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 353 CAALN----GLKMG 362
            + +N     LK+G
Sbjct: 68  ESQINFHGKKLKLG 81

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           +++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A  
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 355 ALNGLKMGDKTLTVR---RATASSGQS 378
                 MG K    R   R + SSG S
Sbjct: 71  MHFHDIMGKKVEVKRAEPRDSKSSGPS 97

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 35/77 (45%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 356 LNGLKMGDKTLTVRRAT 372
           + G  +G + +    AT
Sbjct: 77  MGGQWLGGRQIRTNWAT 93

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE   K L E +G      + +DR      G+GF   +   + +IA A 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAE 77
Query: 356 LNGLKMGDKTLTVRRAT 372
           L+G  +  + L +R AT
Sbjct: 78  LDGTILKSRPLRIRFAT 94

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 39/88 (44%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VFVG L    T   IK     FG +    +VKD  TG SKGYGF  + +    + A   +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQES 384
            G  +G + +    AT      K+  ES
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYES 105

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC-VYQDPAVTDIA 352
           P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF   Y D  V  I 
Sbjct: 10  PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 68
Query: 353 CAALN 357
            + +N
Sbjct: 69  ESQIN 73

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 40/79 (50%)
Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   +
Sbjct: 18  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 357 NGLKMGDKTLTVRRATASS 375
           + +K+  K + V +A+A +
Sbjct: 78  DMIKLYGKPIRVNKASAHN 96

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 6/81 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA   
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 356 LNGLKMGDKTLTVRRATASSG 376
           L+ + +  K L VR A  S+ 
Sbjct: 78  LDNMPLRGKQLRVRFACHSAS 98

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  D A 
Sbjct: 29  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAR 86
Query: 354 AALNGLKMGDKTLTVRRATA 373
             L+G  +  + + V  ATA
Sbjct: 87  EKLHGTVVEGRKIEVNNATA 106

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  D A 
Sbjct: 15  PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAR 72
Query: 354 AALNGLKMGDKTLTVRRATA 373
             L+G  +  + + V  ATA
Sbjct: 73  EKLHGTVVEGRKIEVNNATA 92

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +  T+  ++     +G +    ++KD+ T  S+G+GF  ++DP       A+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 356 ----LNGLKMGDKTLTVR 369
               L+G  +  K  T R
Sbjct: 78  RPHTLDGRNIDPKPCTPR 95

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD      KG+GF   +   + +IA   
Sbjct: 17  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 356 LNGLKMGDKTLTVRRATASS 375
           L+ + +  K L VR A  S+
Sbjct: 71  LDNMPLRGKQLRVRFACHSA 90

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           ++FVG +P    E  +K L E FG ++   ++KDR TG  KG  F  Y
Sbjct: 17  KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 42.0 bits (97), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 33/60 (55%)
Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A AA
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	435
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-73
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-14
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	8e-07
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-32
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-20
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-31
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-28
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-06
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-28
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-21
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-23
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-04
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-10
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-14
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	5e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-18
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-21
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-13
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-20
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-09
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	3e-20
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	9e-09
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-15
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-04
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-18
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-18
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-06
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	4e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-18
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	7e-07
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-08
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-09
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	6e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	8e-18
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	9e-09
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-17
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	9e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-09
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-16
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-07
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-16
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	6e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	2e-16
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	5e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-16
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	5e-16
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-16
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-16
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-05
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-06
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	6e-16
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	8e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	1e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-06
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-06
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-15
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	3e-09
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-15
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-15
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-07
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-15
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	4e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	7e-05
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	9e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-05
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-15
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-07
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-14
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-07
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-07
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-14
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-14
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-07
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-07
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-14
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	6e-07
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-09
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-08
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-05
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-14
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-07
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-07
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	8e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-04
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-14
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-06
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-14
2div_A	99	TRNA selenocysteine associated protein; structural	9e-14
2div_A	99	TRNA selenocysteine associated protein; structural	1e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	9e-14
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	6e-07
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	9e-14
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-13
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	6e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-13
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-06
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-07
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-10
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-13
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-07
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-13
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	5e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	6e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	8e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-12
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-06
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-07
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-12
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-07
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	6e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	8e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	9e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-05
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-11
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-11
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-08
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-08
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-08
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-11
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-05
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	6e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	5e-07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-10
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-07
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	8e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-04
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-04
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-09
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	9e-08
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	5e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	4e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-09
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-09
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	6e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-09
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-08
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-09
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-09
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-08
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-04
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	6e-07
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-06
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	4e-08
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	6e-06
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-07
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	6e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-07
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-05
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-04
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-06
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-05
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-06
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	5e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-06
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-07
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-07
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	8e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-04
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	1e-04
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-06
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	4e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	9e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	6e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	5e-04

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score =  227 bits (581), Expect = 3e-73
 Identities = 91/205 (44%), Positives = 126/205 (61%), Gaps = 10/205 (4%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQMR-LGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P    +  P    P +    V          + 
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVV---------PDS 113

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

Query: 354 AALNGLKMGDKTLTVRRATASSGQS 378
           A LNG+++GDK L V+RA+  +  +
Sbjct: 174 AGLNGMQLGDKKLLVQRASVGAKNA 198

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 70.4 bits (173), Expect = 3e-14
 Identities = 18/94 (19%), Positives = 35/94 (37%), Gaps = 6/94 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
            A A  +G+    ++L +RR           +  
Sbjct: 66  QAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENP 98

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  201 bits (514), Expect = 1e-63
 Identities = 89/199 (44%), Positives = 119/199 (59%), Gaps = 30/199 (15%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M  +GG +  PG+ V+ V IN +K FAF+E R+V+
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQM-RLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEG 293
           E + AMA DGIIF+G ++++RRP DY P                               G
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL-----------------------------PG 93

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A 
Sbjct: 94  AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153

Query: 354 AALNGLKMGDKTLTVRRAT 372
           A LNG+++GDK L V+RA+
Sbjct: 154 AGLNGMQLGDKKLLVQRAS 172

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 70.3 bits (173), Expect = 2e-14
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 6/90 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKT 380
            A  A +G+    ++L +RR          
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGA 94

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 48.0 bits (115), Expect = 8e-07
 Identities = 21/127 (16%), Positives = 42/127 (33%), Gaps = 25/127 (19%)

Query: 141 PEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ--- 197
            +     + F         L   +    Q    A ++++GGLP   N+  +    +    
Sbjct: 61  VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGP 120

Query: 198 -----VMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA 250
                ++  +  G S G               +AF E   +     A+A L+G+      
Sbjct: 121 LKAFNLVKDSATGLSKG---------------YAFCEYVDINVTDQAIAGLNGMQLGDKK 165

Query: 251 VRVRRPT 257
           + V+R +
Sbjct: 166 LLVQRAS 172

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  122 bits (309), Expect = 3e-32
 Identities = 47/229 (20%), Positives = 73/229 (31%), Gaps = 52/229 (22%)

Query: 162 PVQVM---TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            ++     T++  R+ R++ + GLP     Q +    S                +   ++
Sbjct: 7   EIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSD----YE---------LKYCFV 53

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
           +  K  AFV +   E+A  A+ A          + V+                       
Sbjct: 54  DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDA----------------- 96

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 337
                              + V  LP   T+ Q +EL+  FG+L    LV    TG SKG
Sbjct: 97  ------------------LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138

Query: 338 YGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESIL 386
           YGF  Y        A + L G  +G +TL V    A            L
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCL 187

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 90.4 bits (225), Expect = 1e-20
 Identities = 42/235 (17%), Positives = 63/235 (26%), Gaps = 44/235 (18%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---I 218
            + V  Q        + V  LPP   +Q                  G  +    VY    
Sbjct: 86  ELSVQLQP---TDALLCVANLPPSLTQQQFEELVRP---------FGSLERCFLVYSERT 133

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
              K + F E    + A+ A   L G       + V                GQ +P L 
Sbjct: 134 GQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD-----------AGQLTPALL 182

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ-IKELLESFGTLHGFDLVKDRDTGNSK 336
            +                 + V  LP  F +   +   L +  +     L      G  K
Sbjct: 183 HSR---------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLK 226

Query: 337 GYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
           G+    Y+   + + A    +GL +G   L V                I AQA  
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score =  114 bits (287), Expect = 2e-31
 Identities = 39/85 (45%), Positives = 56/85 (65%), Gaps = 1/85 (1%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
             ARR+YVG +P    E+A+  FF+  M   G     PG+ V+ V IN +K FAF+E R+
Sbjct: 4   GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRS 62

Query: 232 VEEASNAMALDGIIFEGVAVRVRRP 256
           V+E + AMA DGIIF+G ++++RRP
Sbjct: 63  VDETTQAMAFDGIIFQGQSLKIRRP 87

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHG-----FDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G      + V        K + F  ++    T 
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 351 IACAALNGLKMGDKTLTVRR 370
               A +G+    ++L +RR
Sbjct: 68  -QAMAFDGIIFQGQSLKIRR 86

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  110 bits (278), Expect = 1e-28
 Identities = 48/212 (22%), Positives = 83/212 (39%), Gaps = 37/212 (17%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
           Q A     RVYVG +     E  I   F+           GP   + ++ +         
Sbjct: 22  QGALAIMSRVYVGSIYYELGEDTIRQAFAP---------FGP---IKSIDMSWDSVTMKH 69

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAA 280
           K FAFVE    E A  A+  ++ ++  G  ++V RP++            + +       
Sbjct: 70  KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA----- 124

Query: 281 VGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
                         +R++V  +    ++  IK + E+FG +    L +D  TG  KGYGF
Sbjct: 125 -------------FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF 171

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             Y+    +  A +++N   +G + L V +A 
Sbjct: 172 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.7 bits (192), Expect = 1e-16
 Identities = 23/96 (23%), Positives = 39/96 (40%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G      RV+VG + Y   E  I++    FG +   D+  D  T   KG+ F  Y+ P  
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             +A   +N + +G + + V R +          + 
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 118

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 46.2 bits (110), Expect = 6e-06
 Identities = 18/119 (15%), Positives = 37/119 (31%), Gaps = 25/119 (21%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDA 212
           P+     +  R   R+YV  +    ++  I + F          +      G   G    
Sbjct: 113 PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG---- 168

Query: 213 VVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPG 270
                      + F+E    + + +A+ +++     G  +RV +       L     PG
Sbjct: 169 -----------YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 216

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  108 bits (272), Expect = 4e-28
 Identities = 27/210 (12%), Positives = 67/210 (31%), Gaps = 55/210 (26%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEK 222
           +     +++G L P  +   +    S+        V+    G +               +
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN---------------R 54

Query: 223 KFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVG 282
           KF +V+  + E+   A+ L G+   G  +++ +P              +   +       
Sbjct: 55  KFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP--------------KGRDSKK----- 95

Query: 283 LASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
                         +    L +  TE ++KE+ E        ++      G SKG  +  
Sbjct: 96  --------VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIE 142

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           ++  A  +       G ++  +++++    
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 49.9 bits (120), Expect = 2e-07
 Identities = 15/93 (16%), Positives = 29/93 (31%), Gaps = 20/93 (21%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQ----VMTAIGGNSAGPGDAVVNVYINHEKK 223
            +  R AR +    L     E  +   F       + +  G S G               
Sbjct: 93  SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG--------------- 137

Query: 224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
            A++E ++  +A   +    G   +G +V +  
Sbjct: 138 IAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  103 bits (258), Expect = 5e-25
 Identities = 30/212 (14%), Positives = 63/212 (29%), Gaps = 52/212 (24%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMRTV 232
           V V  LP   N+  +  +F            GP   +++V +        +FA +E    
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKH---------CGP---IIHVDVADSLKKNFRFARIEFARY 91

Query: 233 EEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 292
           + A  A+     +     + V   T+                                  
Sbjct: 92  DGALAAITKTHKVVGQNEIIVSHLTECT-------------------------------- 119

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
               +++   P  +T+  I++LL+    +     +       S+ + +            
Sbjct: 120 ----LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYC 175

Query: 353 CAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
              LNGLK+   TL  + +       +T+  +
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSAT 207

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 92.4 bits (230), Expect = 3e-21
 Identities = 28/206 (13%), Positives = 67/206 (32%), Gaps = 42/206 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
             +++   PP   ++ I      +               + +          FA++++ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDI---------NVVALSIRLPSLRFNTSRRFAYIDVTS 168

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGG 290
            E+A   +  L+G+  EG  +  +     NP   +            +            
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKV---SNPLEKSKRTDSATLEGREI------------ 213

Query: 291 AEGPDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAV 348
                   +  L      E  ++E  E FG++   ++   +     +    F V+++   
Sbjct: 214 -------MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK-- 264

Query: 349 TDIACAA--LNGLKMGDKTLTVRRAT 372
            D A  A  +N   +G++ ++V  A 
Sbjct: 265 -DSAERALQMNRSLLGNREISVSLAD 289

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 51.1 bits (123), Expect = 2e-07
 Identities = 14/103 (13%), Positives = 30/103 (29%), Gaps = 26/103 (25%)

Query: 167 TQQATRHARRVYVGGLPP-LANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 217
           T  AT   R + +  L   L +E  +   F          +      +            
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEH------------ 250

Query: 218 INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV----RRP 256
            +     AF+     + A  A+ ++  +     + V    ++P
Sbjct: 251 -SFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKKP 292

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  100 bits (252), Expect = 2e-24
 Identities = 38/259 (14%), Positives = 71/259 (27%), Gaps = 58/259 (22%)

Query: 159 PLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI 218
            +       ++      R++VG LP    E+     F +          G       V+I
Sbjct: 7   DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFER---------YGE---PSEVFI 54

Query: 219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLN 277
           N ++ F F+ + +   A  A   LDG I +   +R+R                     L 
Sbjct: 55  NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF--------------ATHGAAL- 99

Query: 278 LAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKG 337
                                V  L    +   +++    FG +    +V D D G + G
Sbjct: 100 --------------------TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATG 138

Query: 338 YGFCVYQDPAVTDIACAALNG----LKMGDKTLTVRRATASSGQSKTEQESILAQAQQHI 393
            GF  +        A          L    + + V        +   +++ +  +  Q  
Sbjct: 139 KGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPM-----EQFDDEDGLPEKLMQKT 193

Query: 394 AIQKMALQTSGMNTLGGGM 412
                  +        G  
Sbjct: 194 QQYHKEREQPPRFAQPGTF 212

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 95.7 bits (239), Expect = 1e-23
 Identities = 35/204 (17%), Positives = 71/204 (34%), Gaps = 50/204 (24%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           + V  LP    ++   + F            G    + +  +           + FV   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGS---------IGE---IESCKLVRDKITGQSLGYGFVNYI 52

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
             ++A  A+  L+G+  +   ++V                 +PS                
Sbjct: 53  DPKDAEKAINTLNGLRLQTKTIKVSYA--------------RPS---------------S 83

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
            +     ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      
Sbjct: 84  ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143

Query: 350 DIACAALNG--LKMGDKTLTVRRA 371
           + A   LNG       + +TV+ A
Sbjct: 144 EEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 81.1 bits (201), Expect = 2e-18
 Identities = 31/84 (36%), Positives = 43/84 (51%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 357 NGLKMGDKTLTVRRATASSGQSKT 380
           NGL++  KT+ V  A  SS   + 
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRD 88

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 41.4 bits (98), Expect = 1e-04
 Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 30/108 (27%)

Query: 162 PVQVMTQQATR---HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGP 209
            ++V   + +        +YV GLP    ++ +   FSQ        ++   + G S G 
Sbjct: 73  TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG- 131

Query: 210 GDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV--AVRVR 254
                           F+      EA  A+  L+G    G    + V+
Sbjct: 132 --------------VGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK 165

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 92.7 bits (231), Expect = 2e-23
 Identities = 26/89 (29%), Positives = 44/89 (49%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++G +PY  TE QI +L  + G +    ++ D  TG SKGY F  ++D   +  A   
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           LNG ++G + L    ++ S     + +  
Sbjct: 64  LNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 21/94 (22%), Positives = 43/94 (45%), Gaps = 19/94 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFV 227
           +R VY+G +P    E+ I    S V         GP   V+N+ +  + +      +AF+
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNV---------GP---VINLKMMFDPQTGRSKGYAFI 49

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYN 260
           E R +E +++A+  L+G       ++    ++ +
Sbjct: 50  EFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 94.5 bits (236), Expect = 3e-23
 Identities = 40/204 (19%), Positives = 72/204 (35%), Gaps = 45/204 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEM 229
           R +YVG L     E  +  +F            GP   + N+ I  +K      +AFVE 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQV---------GGP---IANIKIMIDKNNKNVNYAFVEY 48

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
               +A+ A+  L+G   E   V++                   S   +           
Sbjct: 49  HQSHDANIALQTLNGKQIENNIVKINWA--------------FQSQQSS----------- 83

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
             ++    +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +     
Sbjct: 84  --SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD 141

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
              A  ++ G  +  + L +  A 
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAA 165

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 68.3 bits (168), Expect = 7e-14
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  +K+  +  G +    ++ D+    +  Y F  Y      +IA   L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESI 385
           NG ++ +  + +  A  S   S  +  ++
Sbjct: 62  NGKQIENNIVKINWAFQSQQSSSDDTFNL 90

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 94.2 bits (235), Expect = 5e-23
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 50/204 (24%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMR 230
           + V  LP    ++ +   F            GP   +    I       +   +AFV+  
Sbjct: 6   LIVNYLPQDMTDRELYALFRA---------IGP---INTCRIMRDYKTGYSYGYAFVDFT 53

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           +  ++  A+  L+GI      ++V            A   G+   + NL           
Sbjct: 54  SEMDSQRAIKVLNGITVRNKRLKVSY----------ARPGGESIKDTNL----------- 92

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
                   +V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y      
Sbjct: 93  --------YVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144

Query: 350 DIACAALNG--LKMGDKTLTVRRA 371
             A +ALN    + G + L+VR A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 79.9 bits (198), Expect = 7e-18
 Identities = 22/84 (26%), Positives = 37/84 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 357 NGLKMGDKTLTVRRATASSGQSKT 380
           NG+ + +K L V  A       K 
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKD 89

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 91.6 bits (228), Expect = 7e-22
 Identities = 42/209 (20%), Positives = 70/209 (33%), Gaps = 48/209 (22%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKK 223
             R++++GGL     ++++ + F Q        VM       S G               
Sbjct: 12  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG--------------- 56

Query: 224 FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGL 283
           F FV   TVEE   AM       +G  V  +R         A        P         
Sbjct: 57  FGFVTYATVEEVDAAMNARPHKVDGRVVEPKR---------AVSREDSQRP--------- 98

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
                G      ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  +
Sbjct: 99  -----GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            D    D          +      VR+A 
Sbjct: 154 DDHDSVDKIVIQ-KYHTVNGHNCEVRKAL 181

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 65.8 bits (161), Expect = 8e-13
 Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 1/88 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSK 379
           A  A    K+  + +  +RA +     +
Sbjct: 71  AMNA-RPHKVDGRVVEPKRAVSREDSQR 97

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 89.9 bits (224), Expect = 2e-21
 Identities = 36/204 (17%), Positives = 68/204 (33%), Gaps = 49/204 (24%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
            ++++GGL     E  +  +F +          G    V ++ I  +        F F+ 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGK---------YGT---VTDLKIMKDPATGRSRGFGFLS 51

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAI 288
                     +    I+ +G  +  +R             P                   
Sbjct: 52  FEKPSSVDEVVKTQHIL-DGKVIDPKRAI-----------PRDEQDK------------- 86

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
                  ++FVGG+       + +E    +GT+    L+ D+DTG S+G+GF  Y     
Sbjct: 87  -----TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            D  C     +   D+ + ++RA 
Sbjct: 142 VDRVC-QNKFIDFKDRKIEIKRAE 164

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 67.9 bits (167), Expect = 1e-13
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++E    +GT+    ++KD  TG S+G+GF  ++ P+  D     
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64

Query: 356 LNGLKMGDKTLTVRRATASSGQSKT 380
            +   +  K +  +RA     Q KT
Sbjct: 65  QH--ILDGKVIDPKRAIPRDEQDKT 87

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 84.6 bits (210), Expect = 2e-20
 Identities = 34/76 (44%), Positives = 42/76 (55%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG +   + L V  A
Sbjct: 70  LNGREFSGRALRVDNA 85

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 33/109 (30%), Positives = 50/109 (45%), Gaps = 20/109 (18%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FA 225
           R  R V+VG +P  A E+ +   FS+V         GP   VV+  + ++++      + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEV---------GP---VVSFRLVYDRETGKPKGYG 53

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDY-NPTLAAALGPGQP 272
           F E +  E A +AM  L+G  F G A+RV       N     +LG G P
Sbjct: 54  FCEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 83.8 bits (208), Expect = 3e-20
 Identities = 21/90 (23%), Positives = 38/90 (42%), Gaps = 2/90 (2%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
            S  + G   P    V+V  LP+  T   +  +   +G +    ++KD+DT  SKG  F 
Sbjct: 4   GSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFI 63

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           ++ D         A+N  ++  + +    A
Sbjct: 64  LFLDKDSAQNCTRAINNKQLFGRVIKASIA 93

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.5 bits (124), Expect = 9e-09
 Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 19/88 (21%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 226
               VYV  LP       +   FS+            G  VV V I  +K        AF
Sbjct: 15  SKSTVYVSNLPFSLTNNDLYRIFSKY-----------GK-VVKVTIMKDKDTRKSKGVAF 62

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +     + A N   A++     G  ++ 
Sbjct: 63  ILFLDKDSAQNCTRAINNKQLFGRVIKA 90

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 85.4 bits (212), Expect = 9e-20
 Identities = 39/210 (18%), Positives = 71/210 (33%), Gaps = 50/210 (23%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--------FA 225
           A +++VG +P   +E+ +   F Q          G    V  + +  ++           
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQ---------YGA---VYEINVLRDRSQNPPQSKGCC 50

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
           FV   T + A  A  AL  +                  L     P Q  P         A
Sbjct: 51  FVTFYTRKAALEAQNALHNMK----------------VLPGMHHPIQMKP---------A 85

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
                 A    ++F+G +    TE  I+ +  SFG +    +++    G S+G  F  + 
Sbjct: 86  DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT 144

Query: 345 DPAVTDIACAALNG---LKMGDKTLTVRRA 371
             A+   A  A++    ++     + V+ A
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 71.5 bits (176), Expect = 7e-15
 Identities = 20/93 (21%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTD 350
              ++FVG +P  ++E  ++EL E +G ++  ++++DR      SKG  F  +       
Sbjct: 2   DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQE 383
            A  AL+ +K+        +   +  +     E
Sbjct: 62  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 83.5 bits (207), Expect = 1e-18
 Identities = 42/217 (19%), Positives = 79/217 (36%), Gaps = 49/217 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             +YVG L P   E  +   FS          AGP   ++++ +  +        +A+V 
Sbjct: 16  ASLYVGDLHPDVTEAMLYEKFSP---------AGP---ILSIRVCRDMITRRSLGYAYVN 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 287
            +   +A  A+  ++  + +G  VR+                 Q  P+L           
Sbjct: 64  FQQPADAERALDTMNFDVIKGKPVRIMWS--------------QRDPSLR---------- 99

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++   
Sbjct: 100 ---KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQE 154

Query: 348 VTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             + A   +NG+ + D+ + V R   S  + + E  +
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFK-SRKEREAELGA 190

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 71.9 bits (177), Expect = 1e-14
 Identities = 20/89 (22%), Positives = 36/89 (40%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESI 385
           N   +  K + +  +       K+   +I
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVGNI 106

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 21/106 (19%), Positives = 38/106 (35%), Gaps = 30/106 (28%)

Query: 162 PVQVMTQQATRHARR-----VYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAG 208
           PV++M  Q     R+     +++  L    + +A+   FS         V+    G+   
Sbjct: 86  PVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--- 142

Query: 209 PGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
                        K + FV   T E A  A+  ++G++     V V
Sbjct: 143 -------------KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 79.1 bits (196), Expect = 2e-18
 Identities = 29/83 (34%), Positives = 43/83 (51%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   ++VG L +  TE  ++ + E FG +    L+KD DTG SKGYGF  + D    
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 350 DIACAALNGLKMGDKTLTVRRAT 372
             A   LNG ++  + + V   T
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVT 83

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 19/87 (21%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           +  +YVG L     E  +   F              G  + N+ +         K + F+
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPF-----------GK-IDNIVLMKDSDTGRSKGYGFI 52

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
                E A  A+  L+G    G  +RV
Sbjct: 53  TFSDSECARRALEQLNGFELAGRPMRV 79

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 80.6 bits (199), Expect = 2e-18
 Identities = 29/114 (25%), Positives = 44/114 (38%), Gaps = 2/114 (1%)

Query: 264 AAALGPGQPSPNLNLAAVGLASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTL 321
               G       L               E      + V  +P    E Q+++L E +G +
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPI 69

Query: 322 HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
               +V DR+T  S+GYGF  +Q  +    A A LNG  + +K L V  A +  
Sbjct: 70  ESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 47.8 bits (114), Expect = 6e-07
 Identities = 28/150 (18%), Positives = 48/150 (32%), Gaps = 24/150 (16%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
            Q+P V    P      L     Q     + P Q          R + V  +P   +E  
Sbjct: 2   SQIPLVSQYDPYGQTAQLQ-QLQQQQQQHIPPTQ--MNPEPDVLRNLMVNYIPTTVDEVQ 58

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG 243
           +   F +     G         + +V I         + + FV+ ++   A  A+  L+G
Sbjct: 59  LRQLFER----YG--------PIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106

Query: 244 IIFEGVAVRVR--RPTDYNPTLAAALGPGQ 271
                  ++V         P +A A+G G 
Sbjct: 107 FNILNKRLKVALAASGHQRPGIAGAVGDGN 136

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 78.8 bits (195), Expect = 3e-18
 Identities = 28/95 (29%), Positives = 51/95 (53%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+ G A    ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
           ++      A  A+NG  +  + + V +A  SS   
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 17/85 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEM 229
            +++VGGL    NEQ++   FS+            G    V V  + E    + F FV  
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKY-----------GQISEVVVVKDRETQRSRGFGFVTF 61

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
             +++A +AM A++G   +G  +RV
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRV 86

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 78.0 bits (193), Expect = 4e-18
 Identities = 28/90 (31%), Positives = 46/90 (51%), Gaps = 2/90 (2%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
            G+ G  ++FV  LP+ FT   +K+     G +   D+    + G SKG G   ++ P V
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEV 60

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQS 378
            + AC  +NG+K+  + + VR    +SG S
Sbjct: 61  AERACRMMNGMKLSGREIDVRIDRNASGPS 90

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 17/86 (19%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEM 229
           A +++V  LP     + +   F++      G+       V+   I  E    K    V+ 
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNEC-----GH-------VLYADIKMENGKSKGCGVVKF 55

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVR 254
            + E A  A   ++G+   G  + VR
Sbjct: 56  ESPEVAERACRMMNGMKLSGREIDVR 81

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 78.1 bits (193), Expect = 4e-18
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQDP 346
           + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + DP
Sbjct: 14  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
                A    +G +     + V  AT
Sbjct: 74  PSAKAAIDWFDGKEFSGNPIKVSFAT 99

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 57.7 bits (140), Expect = 7e-11
 Identities = 22/98 (22%), Positives = 37/98 (37%), Gaps = 13/98 (13%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHE--- 221
             +      ++V GL      +++A +F Q   + T         G  ++N+Y + E   
Sbjct: 7   HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKT-----GQPMINLYTDRETGK 61

Query: 222 -KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 257
            K  A V       A  A+   DG  F G  ++V   T
Sbjct: 62  LKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 78.5 bits (194), Expect = 5e-18
 Identities = 32/103 (31%), Positives = 51/103 (49%)

Query: 270 GQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD 329
           G    + +  A  +A+    G+ GP R++VG L +  TE  ++ + E FG +    L+ D
Sbjct: 2   GHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD 61

Query: 330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            +TG SKGYGF  + D      A   LNG ++  + + V   T
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVT 104

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 18/99 (18%), Positives = 33/99 (33%), Gaps = 19/99 (19%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--- 218
            +    Q+ +    R+YVG L     E  +   F            G    + ++ +   
Sbjct: 14  AMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPF---------GR---IESIQLMMD 61

Query: 219 ---NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
                 K + F+     E A  A+  L+G    G  ++V
Sbjct: 62  SETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 77.6 bits (192), Expect = 5e-18
 Identities = 18/84 (21%), Positives = 36/84 (42%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+  
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
             A  AL    +  +       ++
Sbjct: 61  QKAVTALKASGVQAQMAKQSGPSS 84

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 49.8 bits (120), Expect = 3e-08
 Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 17/90 (18%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFV 227
            +  +Y+ GL P   +Q +                  G  V     ++      K + FV
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPY-----------GKIVSTKAILDKTTNKCKGYGFV 52

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRP 256
           +  +   A  A+ AL     +    +   P
Sbjct: 53  DFDSPSAAQKAVTALKASGVQAQMAKQSGP 82

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 77.7 bits (192), Expect = 6e-18
 Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 1/95 (1%)

Query: 279 AAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
            + G +       E    VFVG L     E  + EL    G L    + KDR+ G  K +
Sbjct: 1   GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSF 59

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           GF  ++ P     A A LNG+++  + + V   ++
Sbjct: 60  GFVCFKHPESVSYAIALLNGIRLYGRPINVSGPSS 94

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 27/98 (27%), Positives = 36/98 (36%), Gaps = 18/98 (18%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NH 220
           M        R V+VG L     E+ +   F Q         AGP   +  V I       
Sbjct: 8   MFPAQEEADRTVFVGNLEARVREEILYELFLQ---------AGP---LTKVTICKDREGK 55

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT 257
            K F FV  +  E  S A+  L+GI   G  + V  P+
Sbjct: 56  PKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 78.1 bits (193), Expect = 6e-18
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 289 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+       A   LNG  +  + ++V    
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 51.9 bits (125), Expect = 9e-09
 Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 24/100 (24%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V G+   A E+ I   F++            G+ + N+++N +++     
Sbjct: 18  QRSVEGWILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLK 65

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 256
            +  VE  T +EA  AM  L+G    G  + V     R P
Sbjct: 66  GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 78.1 bits (193), Expect = 6e-18
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++  +T+ V    
Sbjct: 88  LNGAEIMGQTIQVDWCF 104

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 19/92 (20%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 21  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 68

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
            +A VE  T ++A  A  AL+G    G  ++V
Sbjct: 69  GYALVEYETHKQALAAKEALNGAEIMGQTIQV 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 77.3 bits (191), Expect = 8e-18
 Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
             ++F+ GLP+  T+ +++E+ ++ GT+    LV +R  G  KG  +  Y++ +    A 
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAV 75

Query: 354 AALNGLKMGDKTLTVRRA 371
             ++G+ + +  + V  +
Sbjct: 76  MKMDGMTIKENIIKVAIS 93

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 18/85 (21%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEM 229
            ++++ GLP    ++ +                G    V ++ +        K  A+VE 
Sbjct: 18  HKLFISGLPFSCTKEELEEICKAH---------GT---VKDLRLVTNRAGKPKGLAYVEY 65

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +AS A+  +DG+  +   ++V
Sbjct: 66  ENESQASQAVMKMDGMTIKENIIKV 90

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 78.3 bits (193), Expect = 1e-17
 Identities = 22/105 (20%), Positives = 39/105 (37%), Gaps = 4/105 (3%)

Query: 271 QPSPNLNLAAVGLASGAIGGAEGPD----RVFVGGLPYYFTETQIKELLESFGTLHGFDL 326
               N     V   SG  GG+ G       ++VGGL     +  +      FG +    +
Sbjct: 36  YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95

Query: 327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
             D +T   +G+ F  ++       A   +N  ++  +T+ V  A
Sbjct: 96  PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 52.9 bits (127), Expect = 9e-09
 Identities = 24/130 (18%), Positives = 46/130 (35%), Gaps = 20/130 (15%)

Query: 131 GQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQA 190
            ++  + S +PE          T+            +  +    R +YVGGL    +++ 
Sbjct: 21  DEMYEILSNLPESVA-YTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKV 79

Query: 191 IATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG 243
           +   F            G    + ++ I         + FAFVE    E+A+ A+  ++ 
Sbjct: 80  LHAAFIP---------FGD---ITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 127

Query: 244 IIFEGVAVRV 253
               G  +RV
Sbjct: 128 SELFGRTIRV 137

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 74.6 bits (184), Expect = 9e-17
 Identities = 19/89 (21%), Positives = 37/89 (41%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+ G A     ++VGGL     +  +      FG +    +  D +T   +G+ F  +
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           +       A   +N  ++  +T+ V  A 
Sbjct: 62  ELAEDAAAAIDNMNESELFGRTIRVNLAK 90

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 47.2 bits (113), Expect = 4e-07
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 19/94 (20%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 223
           +       R +YVGGL    +++ +   F            G    + ++ I  + +   
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEK 52

Query: 224 ---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
              FAFVE    E+A+ A+  ++     G  +RV
Sbjct: 53  HRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 74.1 bits (183), Expect = 9e-17
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68

Query: 356 LNGLKMGDKTLTVRRA 371
           +N  ++  +T+ V  A
Sbjct: 69  MNESELFGRTIRVNLA 84

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
           R +YVGGL    +++ +   F            G    + ++ I  + +      FAFVE
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIP---------FGD---ITDIQIPLDYETEKHRGFAFVE 55

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
               E+A+ A+  ++     G  +RV
Sbjct: 56  FELAEDAAAAIDNMNESELFGRTIRV 81

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 22/93 (23%), Positives = 45/93 (48%), Gaps = 3/93 (3%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F
Sbjct: 2   SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
             +++      A    NG+++  + + V   ++
Sbjct: 62  VYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSK---------YGP---IADVSIVYDQQSRRSRGFAFVY 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
              V++A  A    +G+  +G  +RV
Sbjct: 64  FENVDDAKEAKERANGMELDGRRIRV 89

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 28/98 (28%), Positives = 44/98 (44%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG I        V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +
Sbjct: 5   SSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTE 381
                 D A   ++ +K+  K + V +A+A +      
Sbjct: 65  LSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGP 102

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 19/86 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             VYVGGL    +E  +   F Q         AGP   VVN ++  ++       + FVE
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQ---------AGP---VVNTHMPKDRVTGQHQGYGFVE 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
             + E+A  A+  +D I   G  +RV
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPIRV 89

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 73.9 bits (182), Expect = 2e-16
 Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 285 SGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           S    G +  D  ++F+G +P    E  +K L E FG ++   ++KDR TG  KG  F  
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 343 YQDPAVTDIACAALNGLKM---GDKTLTVRRAT 372
           Y +      A +AL+  K     ++ + V+ A 
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 15/98 (15%), Positives = 33/98 (33%), Gaps = 22/98 (22%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NH 220
           +      A ++++G +P   +E+ +   F +      G        +  + +        
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEF-----GK-------IYELTVLKDRFTGM 53

Query: 221 EKKFAFVEMRTVEEASNAM-ALDG---IIFEGVAVRVR 254
            K  AF+     E A  A  AL     +      ++V+
Sbjct: 54  HKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVK 91

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 74.3 bits (183), Expect = 2e-16
 Identities = 33/113 (29%), Positives = 51/113 (45%), Gaps = 1/113 (0%)

Query: 259 YNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESF 318
              + +A       S  L+ AA   A   I G EG   +F+  LP  FT+T +      F
Sbjct: 6   QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGC-NLFIYHLPQEFTDTDLASTFLPF 64

Query: 319 GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           G +    +  D+ T  SK +GF  + +P    +A  A+NG ++G K L V+  
Sbjct: 65  GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 21/131 (16%), Positives = 37/131 (28%), Gaps = 27/131 (20%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
            G+P      A +  P  +  L A          Q        +++  LP    +  +A+
Sbjct: 2   AGLPQFGSASALSTSPLASVALSAAAAAAAG--KQIEGPEGCNLFIYHLPQEFTDTDLAS 59

Query: 194 FFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG 243
            F          V        S                 F FV     + A  A+ A++G
Sbjct: 60  TFLPFGNVISAKVFIDKQTSLSKC---------------FGFVSFDNPDSAQVAIKAMNG 104

Query: 244 IIFEGVAVRVR 254
                  ++V+
Sbjct: 105 FQVGTKRLKVQ 115

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 73.0 bits (180), Expect = 3e-16
 Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG L Y  T  Q+KEL   FG +    L+ DR+T   KG+GF   Q+ +V++ A A 
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAK 61

Query: 356 LNGLKMGDKTLTVRRA 371
           L+      +T+ V  A
Sbjct: 62  LDNTDFMGRTIRVTEA 77

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 20/87 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
           R +YVG L   A  + +   FSQ            G  V NV + ++++      F FVE
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQF-----------GK-VFNVKLIYDRETKKPKGFGFVE 49

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVR 254
           M+  E  S A+  LD   F G  +RV 
Sbjct: 50  MQE-ESVSEAIAKLDNTDFMGRTIRVT 75

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 72.1 bits (178), Expect = 3e-16
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FVG L     +  ++   + F +     ++ D  TG+S+GYGF  +        A  +
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 356 LNGLKMGDKTLTVRRAT 372
           + G  +  + L +  A 
Sbjct: 63  MQGQDLNGRPLRINWAA 79

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 25/88 (28%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            ++VG L    +++ +   F          VM     G+S G               + F
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG---------------YGF 47

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           V   + ++A NAM ++ G    G  +R+
Sbjct: 48  VSFTSQDDAQNAMDSMQGQDLNGRPLRI 75

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 74.5 bits (183), Expect = 5e-16
 Identities = 23/73 (31%), Positives = 34/73 (46%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 356 LNGLKMGDKTLTV 368
           LNG ++  +T+ V
Sbjct: 134 LNGAEIMGQTIQV 146

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 50.2 bits (120), Expect = 1e-07
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 19/92 (20%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK----- 223
           Q +     ++V  +   A E  I   F            G    + N+++N +++     
Sbjct: 67  QRSVEGWILFVTSIHEEAQEDEIQEKFCDY---------GE---IKNIHLNLDRRTGFSK 114

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
            +A VE  T ++A  A  AL+G    G  ++V
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 72.3 bits (178), Expect = 5e-16
 Identities = 16/90 (17%), Positives = 36/90 (40%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           +       A   LN   +G + + +   ++
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 13/86 (15%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTV 232
            + V  +P   +   I  FF                  V +  N +      A V   + 
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 233 EEASNAMA-LDGIIFEGVAVRVRRPT 257
           +EA+ A+  L+        V++  P+
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLSGPS 93

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 73.8 bits (181), Expect = 6e-16
 Identities = 26/114 (22%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 271 QPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVK 328
           +PSP  N     +     G       V+VG   ++ T+ Q+ +++ S G     +    +
Sbjct: 32  EPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE 91

Query: 329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
           +R  G SKGY   V             L G  +  + + VR AT  +      Q
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQ 145

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 46.8 bits (111), Expect = 2e-06
 Identities = 25/121 (20%), Positives = 37/121 (30%), Gaps = 16/121 (13%)

Query: 161 MPVQVMTQQATRHAR-RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYI 218
            P  + T    R+ R  VYVG       +Q +                G  D V +    
Sbjct: 41  TPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRS---------IGVYDVVELKFAE 91

Query: 219 NHE----KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
           N      K +A V + +       +  L G +  G  V VR  T  N +   A    +  
Sbjct: 92  NRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKREC 151

Query: 274 P 274
            
Sbjct: 152 V 152

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 71.9 bits (177), Expect = 6e-16
 Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN---SKGYGFCVYQDP 346
           G+ G   +F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 347 AVTDIACAALNGLKMGDKTLTVRRA 371
                A   L G  +    L VR +
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRIS 85

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 20/89 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            +++  L     E+ +   FS+        +                         F FV
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVL-----------LSMGFGFV 55

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
           E +  E+A  A+  L G   +G  + VR 
Sbjct: 56  EYKKPEQAQKALKQLQGHTVDGHKLEVRI 84

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 72.4 bits (178), Expect = 6e-16
 Identities = 26/106 (24%), Positives = 39/106 (36%), Gaps = 6/106 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +
Sbjct: 5   SSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQF 64

Query: 344 QDPAVTDIACAALN------GLKMGDKTLTVRRATASSGQSKTEQE 383
                     AA +      GLK+  + L V  A      +     
Sbjct: 65  MTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 25/96 (26%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKF 224
               + V++  L   + E+A+     Q          G    +  V +       H K  
Sbjct: 12  VTEGKTVFIRNLSFDSEEEALGEVLQQF---------GD---LKYVRVVLHPDTEHSKGC 59

Query: 225 AFVEMRTVEEASNAMA-------LDGIIFEGVAVRV 253
           AF +  T E A   +A         G+  +G  ++V
Sbjct: 60  AFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 72.4 bits (178), Expect = 6e-16
 Identities = 11/83 (13%), Positives = 25/83 (30%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GG      V    L     ET +K++   +G +   +++    T    G    ++     
Sbjct: 1   GGQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60

Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
                  L+   +    +  +  
Sbjct: 61  AKETVKNLHLTSVMGNIIHAQLD 83

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 51.6 bits (124), Expect = 1e-08
 Identities = 12/93 (12%), Positives = 20/93 (21%), Gaps = 19/93 (20%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAF 226
             + V    L     E  +     +          G    V  V I    +       A 
Sbjct: 5   PLKEVTFARLNDNVRETFLKDMCRKY---------GE---VEEVEILLHPRTRKHLGLAR 52

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
           V   +   A   +  L      G  +  +    
Sbjct: 53  VLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIK 85

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 72.4 bits (178), Expect = 8e-16
 Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 8/86 (9%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQDP 346
             ++V GL    T   + +  +  G +            +  D++TG  KG     Y+DP
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
                A    +G       L V  A 
Sbjct: 76  PTAKAAVEWFDGKDFQGSKLKVSLAR 101

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 7/86 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAFVEMR 230
             +YV GL        +A FF Q    +   +   G  ++++Y++ E    K  A V   
Sbjct: 16  SAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR 255
               A  A+   DG  F+G  ++V  
Sbjct: 74  DPPTAKAAVEWFDGKDFQGSKLKVSL 99

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 71.6 bits (176), Expect = 1e-15
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 1/94 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     +
Sbjct: 5   SSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT-ASSG 376
           +       A   LN   +G + + +   +  SSG
Sbjct: 65  ESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 43.8 bits (104), Expect = 6e-06
 Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 13/83 (15%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           + V  +P   +   I  FF                  V +  N +      A V   + +
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGY---------QVIPGSVCLKYNEKGMPTGEAMVAFESRD 68

Query: 234 EASNAMA-LDGIIFEGVAVRVRR 255
           EA+ A+  L+        V++  
Sbjct: 69  EATAAVIDLNDRPIGSRKVKLVL 91

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 71.5 bits (176), Expect = 1e-15
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 3/92 (3%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G     D    + V  L     ET ++EL   FG++    L KD+ TG SKG+ F
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
             +        A A ++G       L V  A 
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 17/97 (17%), Positives = 36/97 (37%), Gaps = 22/97 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L     E  +   F       G        ++  +Y+  +K       FAF+  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRP----FG--------SISRIYLAKDKTTGQSKGFAFISF 64

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNPT 262
              E+A+ A+  + G  ++ + + V   +  T+  P+
Sbjct: 65  HRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPS 101

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 71.1 bits (175), Expect = 1e-15
 Identities = 23/84 (27%), Positives = 37/84 (44%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
             A A ++G     + L V  +T 
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTI 87

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEM 229
           R++V  L   ++E+ +   FS           GP   +  ++          K FAFV  
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAY---------GP---LSELHYPIDSLTKKPKGFAFVTF 57

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
              E A  A   +DG +F+G  + V
Sbjct: 58  MFPEHAVKAYAEVDGQVFQGRMLHV 82

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 71.7 bits (176), Expect = 1e-15
 Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 8/87 (9%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTL--------HGFDLVKDRDTGNSKGYGFCVYQD 345
            + +FV GL    T   + +  +  G +           +L  DR+TG  KG     + D
Sbjct: 7   NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRAT 372
           P     A    +G +     + V  AT
Sbjct: 67  PPSAKAAIDWFDGKEFSGNPIKVSFAT 93

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 53.6 bits (129), Expect = 3e-09
 Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 14/104 (13%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIG--GNSAGPGDAVVNVYINHE---- 221
           +Q       ++V GL      +++A +F Q    IG    +   G  ++N+Y + E    
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQ----IGIIKTNKKTGQPMINLYTDRETGKL 56

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTDYNP 261
           K  A V       A  A+   DG  F G  ++V    R  D+N 
Sbjct: 57  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNR 100

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 25/90 (27%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 289 GGAEGPDR------VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G   GP R      +FV G+    TE  I +    +G +    L  DR TG  KGY    
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 343 YQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
           Y+       A   LNG  +  + ++V    
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 19/107 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            ++V G+   A E+ I   F++            G+ + N+++N +++      +  VE 
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEY-----------GE-IKNIHLNLDRRTGYLKGYTLVEY 71

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 275
            T +EA  AM  L+G    G  + V       P      G  + S +
Sbjct: 72  ETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRS 118

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 6/117 (5%)

Query: 273 SPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT 332
           S  L   ++G A     G EG   +F+  LP  F +  + ++   FG +    +  D+ T
Sbjct: 5   SSGLTQQSIGAAGSQKEGPEGA-NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63

Query: 333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 389
             SK +GF  Y +P     A  ++NG ++G K L V+       +SK + +S  +  
Sbjct: 64  NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK-----RSKNDSKSGPSSG 115

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 70.4 bits (173), Expect = 4e-15
 Identities = 28/94 (29%), Positives = 46/94 (48%), Gaps = 1/94 (1%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           A+ P ++F+GGL     E  +K +    G +    L+KDR T  S+G+ F  +++PA   
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
            A   +NG  +  K + V +A   S QS   +  
Sbjct: 63  NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 24/109 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++++GGL    NE+ +   F +        ++      S G               FAF+
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG---------------FAFI 53

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPN 275
                 +A NA   ++G    G A++V +    +        P   S N
Sbjct: 54  TFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRN 102

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 70.0 bits (172), Expect = 5e-15
 Identities = 23/109 (21%), Positives = 44/109 (40%), Gaps = 6/109 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SGA+        VFV  L Y     ++KE+    G +   D+++D+D G S+G G   +
Sbjct: 5   SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTF 63

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           +       A +  NG  + D+ + V+       +    +       +  
Sbjct: 64  EQSIEAVQAISMFNGQLLFDRPMHVKMD-----ERALPKGDFFPPERPQ 107

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 20/118 (16%), Positives = 31/118 (26%), Gaps = 26/118 (22%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINH 220
           QA R    V+V  L      + +   FS         ++    G S G            
Sbjct: 10  QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG------------ 57

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNPTLAAALGPGQPSPN 275
                 V      EA  A+   +G +     + V+                P Q  P+
Sbjct: 58  ---IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 69.1 bits (170), Expect = 6e-15
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 290 GAEGPDR-VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G E   R ++VG + Y  T  +++      G+++   ++ D+ +G+ KG+ +  + D   
Sbjct: 1   GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60

Query: 349 TDIACAALNGLKMGDKTLTVRRA 371
              +  AL+      + + V   
Sbjct: 61  VRTS-LALDESLFRGRQIKVIPK 82

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 61.0 bits (149), Expect = 4e-12
 Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 18/88 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           AR +YVG +   A  + +   F              G  V  V I       H K FA++
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGC-----------GS-VNRVTILCDKFSGHPKGFAYI 53

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
           E    E    ++ALD  +F G  ++V  
Sbjct: 54  EFSDKESVRTSLALDESLFRGRQIKVIP 81

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 69.2 bits (170), Expect = 9e-15
 Identities = 24/103 (23%), Positives = 44/103 (42%), Gaps = 7/103 (6%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G  G   +F+  L        + +   +FG +    +V   D   SKGYGF  ++     
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV--CDENGSKGYGFVHFETQEAA 58

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           + A   +NG+ + D+ + V R      +S+ E+E+ L    + 
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRF-----KSRKEREAELGARAKE 96

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 41.1 bits (97), Expect = 7e-05
 Identities = 21/143 (14%), Positives = 38/143 (26%), Gaps = 46/143 (32%)

Query: 177 VYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           +++  L    + +A+   FS         V+    G+                K + FV 
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS----------------KGYGFVH 51

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGA 287
             T E A  A+  ++G++     V V R        A      +   N            
Sbjct: 52  FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTN------------ 99

Query: 288 IGGAEGPDRVFVGGLPYYFTETQ 310
                    V++       T   
Sbjct: 100 ---------VYIKNFGPGSTRAA 113

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 68.8 bits (169), Expect = 9e-15
 Identities = 26/103 (25%), Positives = 42/103 (40%), Gaps = 8/103 (7%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
            G   P+ VFVGG+     ET+I+     +G++    ++ DR TG SKGYGF  + +   
Sbjct: 4   EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVD 62

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
                   + +    K L +  A       K    +   Q + 
Sbjct: 63  VQKIVE--SQINFHGKKLKLGPA-----IRKQNLSTYHVQPRP 98

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 24/88 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            V+VGG+    +E  I +FF++        ++T   G S G               + FV
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG---------------YGFV 55

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
                 +    +    I F G  +++  
Sbjct: 56  SFYNDVDVQKIVE-SQINFHGKKLKLGP 82

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 68.3 bits (168), Expect = 9e-15
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVT 349
           +  P +V +G L    T+  I E+  ++G +   D+  +R     SKGY +  +++P   
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
           + A   ++G ++  + +T     A
Sbjct: 61  EKALKHMDGGQIDGQEITATAVLA 84

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 46.0 bits (110), Expect = 7e-07
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 20/86 (23%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVE 228
           +V++G L     +  I   FS      G         +  + +       +  K +A+VE
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFST----YG--------KIKMIDMPVERMHPHLSKGYAYVE 53

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
               +EA  A+  +DG   +G  +  
Sbjct: 54  FENPDEAEKALKHMDGGQIDGQEITA 79

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 68.4 bits (168), Expect = 1e-14
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            +++G L ++ T+  + E + S G     +    ++R  G SKG+        A +    
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 354 AALNGLKMGDKTLTVRRAT 372
             L   ++  +   V  + 
Sbjct: 63  DLLPKRELHGQNPVVTPSN 81

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 14/94 (14%), Positives = 29/94 (30%), Gaps = 17/94 (18%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEMR 230
            +Y+G L     ++ +      +         G  D + +  + N      K FA V + 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSL---------GVNDILEIKFFENRANGQSKGFALVGVG 53

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVR--RPTDYNP 261
           +   +   M  L      G    V      +++ 
Sbjct: 54  SEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHH 87

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 71.5 bits (175), Expect = 1e-14
 Identities = 35/196 (17%), Positives = 57/196 (29%), Gaps = 25/196 (12%)

Query: 177 VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 53

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS------PNLNLAAVGLASGA 287
           A  AM  L+G    G  +R+      N  L       Q          L+      +   
Sbjct: 54  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 113

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                    + +  +P   +E  +K L  S G +        +D    +           
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVE 169

Query: 348 VTDIACAALNGLKMGD 363
               A   L+   +G+
Sbjct: 170 EAVQALIDLHNHDLGE 185

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 49.9 bits (119), Expect = 2e-07
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 6/89 (6%)

Query: 297 VFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           + V  L P   T   +  L   +G +    ++ +      K        D     +A + 
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           LNG K+  K + +  +   + Q   E + 
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQE 89

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 48.7 bits (116), Expect = 7e-07
 Identities = 26/124 (20%), Positives = 46/124 (37%), Gaps = 13/124 (10%)

Query: 132 QLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           Q   +P    E       +G + L  F   P     Q     +  +++  +PP  +E+ +
Sbjct: 79  QNVQLPREGQEDQGLTKDYGNSPLHRFKK-PGSKNFQNIFPPSATLHLSNIPPSVSEEDL 137

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGV 249
              FS             G      +   ++K A ++M +VEEA  A+  L    + E  
Sbjct: 138 KVLFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENH 187

Query: 250 AVRV 253
            +RV
Sbjct: 188 HLRV 191

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 356 LNGLKMGDKTLTV--------RRATASSG 376
           +NG K+  K L +        R +  SSG
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQRSSGPSSG 115

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 41.9 bits (99), Expect = 4e-05
 Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 13/83 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
           + +Y+  L P   E+ + + F++                   +     +    AF+    
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARF---------QEKKGPPIQFRMMTGRMRGQAFITFPN 76

Query: 232 VEEASNAM-ALDGIIFEGVAVRV 253
            E A  A+  ++G    G  + +
Sbjct: 77  KEIAWQALHLVNGYKLYGKILVI 99

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 71.3 bits (174), Expect = 1e-14
 Identities = 30/204 (14%), Positives = 48/204 (23%), Gaps = 25/204 (12%)

Query: 177 VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V GL     N   +   F        GN       V  V     K   A VEM     
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLY-----GN-------VEKVKFMKSKPGAAMVEMADGYA 54

Query: 235 ASNAM-ALDGIIFEGVAVRVR---------RPTDYNPTLAAALGPGQPSPNLNLAAVGLA 284
              A+  L+     G  + V            +      + +      S N   +    A
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQA 114

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           +           +     P   TE    E+ +  G      +            G   + 
Sbjct: 115 AKNRIQHPSN-VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWD 173

Query: 345 DPAVTDIACAALNGLKMGDKTLTV 368
             +        LN  +M +     
Sbjct: 174 SKSDALETLGFLNHYQMKNPNGPY 197

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 47.8 bits (113), Expect = 2e-06
 Identities = 16/110 (14%), Positives = 30/110 (27%), Gaps = 7/110 (6%)

Query: 290 GAEGPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           GA+ P  + V GL        ++  +   +G +     +K +      G       D   
Sbjct: 1   GADSP-VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYA 54

Query: 349 TDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKM 398
            D A   LN   M  + + V  +   +                    +  
Sbjct: 55  VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESR 104

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 42.8 bits (100), Expect = 8e-05
 Identities = 14/123 (11%), Positives = 36/123 (29%), Gaps = 8/123 (6%)

Query: 127 AAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLA 186
           +  P  +PG    + + + +   F  ++   F   P Q    +    +  ++    P   
Sbjct: 77  SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFS-TPEQAAKNRIQHPSNVLHFFNAPLEV 135

Query: 187 NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGII 245
            E+       ++          P    V    +       +E  +  +A   +  L+   
Sbjct: 136 TEENFFEICDEL------GVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ 189

Query: 246 FEG 248
            + 
Sbjct: 190 MKN 192

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 68.9 bits (169), Expect = 1e-14
 Identities = 18/98 (18%), Positives = 40/98 (40%), Gaps = 3/98 (3%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
             +++  LPY  T  ++ ++   +G +    +     T  ++G  + VY+D      A  
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 355 ALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
            L+G  + ++ L V    A+    K + +    Q +  
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 103

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRT 231
           R +Y+  LP     + +   F +          GP   +  + + +  +    A+V    
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKY---------GP---IRQIRVGNTPETRGTAYVVYED 56

Query: 232 VEEASNAM-ALDGIIFEGVAVRV 253
           + +A NA+  L G       + V
Sbjct: 57  IFDAKNAVDHLSGFNVSNRYLVV 79

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 68.5 bits (168), Expect = 1e-14
 Identities = 31/101 (30%), Positives = 42/101 (41%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          VFVG L    T   IK     FG +    +VKD  TG SKGYGF  +
Sbjct: 5   SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
            +    + A   + G  +G + +    AT      K+  ES
Sbjct: 65  FNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 40.8 bits (96), Expect = 8e-05
 Identities = 24/112 (21%), Positives = 35/112 (31%), Gaps = 29/112 (25%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            V+VG L P    + I   F+         V+     G S G               + F
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG---------------YGF 61

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRPTDYNPTLAAALGPGQPS 273
           V      +A NA+  + G    G  +R     R+P     T  +      PS
Sbjct: 62  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPS 113

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 5/88 (5%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
                 +    L +  TE ++KE+ E        ++      G SKG  +  ++  A  +
Sbjct: 13  VRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAE 67

Query: 351 IACAALNGLKMGDKTLTVRRATASSGQS 378
                  G ++  +++++       G  
Sbjct: 68  KNLEEKQGAEIDGRSVSLYYTGEKGGTR 95

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 12/88 (13%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           T +  R AR +    L     E  +   F               +  +       K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDA-----------LEIRLVSQDGKSKGIAY 57

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +E ++  +A   +    G   +G +V +
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSL 85

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 18/91 (19%), Positives = 40/91 (43%)

Query: 282 GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           G +  +    +G   + V  L Y  +   ++ + E +G +    + ++  T   +G+ F 
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRAT 372
            + D      A AA++G ++  + L V+ A 
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRVQVAR 91

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 19/85 (22%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L    +  ++   F +          G    V +VYI  E        FAFV  
Sbjct: 15  TLKVDNLTYRTSPDSLRRVFEK---------YGR---VGDVYIPREPHTKAPRGFAFVRF 62

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +A +A  A+DG   +G  +RV
Sbjct: 63  HDRRDAQDAEAAMDGAELDGRELRV 87

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 68.6 bits (168), Expect = 2e-14
 Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VG + Y  T   ++    S G+++   ++ D+ +G+ KGY +  + +    D A  A
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-VA 96

Query: 356 LNGLKMGDKTLTVRRA 371
           ++      +T+ V   
Sbjct: 97  MDETVFRGRTIKVLPK 112

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 58.6 bits (142), Expect = 6e-11
 Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 18/94 (19%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
           ++     R VYVG +   +  Q +   FS           G    +  + I       H 
Sbjct: 30  EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC---------GS---INRITILCDKFSGHP 77

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K +A++E         A+A+D  +F G  ++V  
Sbjct: 78  KGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 2/96 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG +     P  ++VG L    TE  I +L    G      ++ +  +     Y F  +
Sbjct: 5   SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
            +      A AA+NG K+  K + V  AT  S Q  
Sbjct: 63  YEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.6 bits (127), Expect = 5e-09
 Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 17/91 (18%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---- 223
            +     R +YVG L     E  I   FSQ          GP     +  +  E      
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQ---------IGP---CKSCKMITEHTSNDP 56

Query: 224 FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           + FVE     +A+ A+ A++G    G  V+V
Sbjct: 57  YCFVEFYEHRDAAAALAAMNGRKILGKEVKV 87

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 11/94 (11%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G +++++G L    T   +++L           L          GY F  Y D    
Sbjct: 4   GSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWA 57

Query: 350 DIACAALNG-LKMGDKTLTVRRATA----SSGQS 378
             A   L+G +++  K + V  + +    SSG S
Sbjct: 58  IRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            ++Y+G L P      +   F                  +   +  +  +AFV+      
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGD----RKL--------PLAGQVLLKSGYAFVDYPDQNW 56

Query: 235 ASNAM-ALDGII-FEGVAVRVR 254
           A  A+  L G +   G  + V 
Sbjct: 57  AIRAIETLSGKVELHGKIMEVD 78

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 1/84 (1%)

Query: 290 GAEGPD-RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G  G    VFVG L    T   I      FG +    +VKD  TG SKGYGF  + +   
Sbjct: 1   GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            + A   + G  +G + +    AT
Sbjct: 61  AENAIQQMGGQWLGGRQIRTNWAT 84

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 23/95 (24%), Positives = 32/95 (33%), Gaps = 29/95 (30%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMT-AIGGNSAGPGDAVVNVYINHEKKFAF 226
            V+VG L P     AIA  F+         V+     G S G               + F
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG---------------YGF 52

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV----RRP 256
           V      +A NA+  + G    G  +R     R+P
Sbjct: 53  VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 23/97 (23%), Positives = 46/97 (47%), Gaps = 2/97 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG       P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTF 62

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKT 380
           ++ A  D A   L+G  +  + + V  ATA    +  
Sbjct: 63  ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 17/84 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMR 230
           +R++V  +P    +  +   F Q          G    +++V I       K F FV   
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGSKGFGFVTFE 63

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
              +A  A   L G + EG  + V
Sbjct: 64  NSADADRAREKLHGTVVEGRKIEV 87

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 67.3 bits (165), Expect = 3e-14
 Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG    +     + +  L Y  TE  ++E+ E    +     V     G SKGY F  +
Sbjct: 5   SSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEF 60

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
                   A  + N  ++  + + +    
Sbjct: 61  ASFEDAKEALNSCNKREIEGRAIRLELQG 89

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 21/86 (24%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQ-----VMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           ++ + +  L   A E+ +   F +     V     G S G               +AF+E
Sbjct: 15  SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKG---------------YAFIE 59

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV 253
             + E+A  A+ + +    EG A+R+
Sbjct: 60  FASFEDAKEALNSCNKREIEGRAIRL 85

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 67.3 bits (165), Expect = 4e-14
 Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 1/90 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 19  GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHF 77

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           +  A    A    NG+ +  + + ++  T+
Sbjct: 78  ERKADALKAMKQYNGVPLDGRPMNIQLVTS 107

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 24/88 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG---------------TADV 75

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVR 254
                 +A  AM   +G+  +G  + ++
Sbjct: 76  HFERKADALKAMKQYNGVPLDGRPMNIQ 103

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 67.8 bits (166), Expect = 4e-14
 Identities = 22/105 (20%), Positives = 40/105 (38%), Gaps = 6/105 (5%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
             G   G E   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     +
Sbjct: 25  GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 388
           +  A    A     G+ +  + + ++        S+ + E     
Sbjct: 84  ERRADALKAMKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHHH 123

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 15/87 (17%), Positives = 26/87 (29%), Gaps = 24/87 (27%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++ V  L    ++  I   F++        V     G S G                A V
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG---------------TADV 81

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
                 +A  AM    G+  +G  + +
Sbjct: 82  HFERRADALKAMKQYKGVPLDGRPMDI 108

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 67.3 bits (165), Expect = 5e-14
 Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 4/93 (4%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
            S  + G++       +FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATA 373
               D A  + AC   N +  G +   V  A  
Sbjct: 64  VTMADRAAAERACKDPNPIIDG-RKANVNLAYL 95

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 67.4 bits (165), Expect = 6e-14
 Identities = 17/81 (20%), Positives = 38/81 (46%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++      
Sbjct: 44  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A    NG+++  + + V  + 
Sbjct: 104 AKERANGMELDGRRIRVDFSI 124

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 24/94 (25%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
             + V GL     E+ +   FS+          GP   + +V I ++++      FAFV 
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKY---------GP---IADVSIVYDQQSRRSRGFAFVY 94

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV-----RRP 256
              V++A  A    +G+  +G  +RV     +RP
Sbjct: 95  FENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 66.4 bits (163), Expect = 7e-14
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGG+P+   ET+++E  + FG +    ++ D +    +G+GF  ++D    D A   
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
            +   +  K + V+RA     +S 
Sbjct: 72  -HFHDIMGKKVEVKRAEPRDSKSS 94

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 18/87 (20%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK----FAFVE 228
            +++VGG+P    E  +  +F +      G        V  V +  + EK+    F F+ 
Sbjct: 11  NKIFVGGIPHNCGETELREYFKKF-----GV-------VTEVVMIYDAEKQRPRGFGFIT 58

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRR 255
               +    A+ +      G  V V+R
Sbjct: 59  FEDEQSVDQAVNMHFHDIMGKKVEVKR 85

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 66.5 bits (163), Expect = 7e-14
 Identities = 23/98 (23%), Positives = 42/98 (42%), Gaps = 5/98 (5%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G      +   + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
             + +        +  +   +  +    +   +   Q 
Sbjct: 62  VRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQD 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 65.8 bits (161), Expect = 9e-14
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQ 344
           G+ G +     +++G L  Y  E  I     + G T+    ++++R TG   GY F  + 
Sbjct: 1   GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60

Query: 345 DPAVTDIACAALNGLKMGDKTLTVR 369
           D A  +     +NG  +   T   R
Sbjct: 61  DLATAEKCLHKINGKPLPGATPAKR 85

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 18/88 (20%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFV 227
           A  +++G L P  +E  I+  F+ +           G+ V++V I           + FV
Sbjct: 9   AASLWMGDLEPYMDENFISRAFATM-----------GETVMSVKIIRNRLTGIPAGYCFV 57

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           E   +  A   +  ++G    G     R
Sbjct: 58  EFADLATAEKCLHKINGKPLPGATPAKR 85

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 67.6 bits (165), Expect = 9e-14
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
            EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D    +
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
            A  A++G  +  + L V+ A 
Sbjct: 127 DAMDAMDGAVLDGRELRVQMAR 148

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 47.9 bits (114), Expect = 6e-07
 Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 24/99 (24%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVEM 229
            + V  L    +   +   F +          G    V +VYI  ++       FAFV  
Sbjct: 72  SLKVDNLTYRTSPDTLRRVFEK---------YGR---VGDVYIPRDRYTKESRGFAFVRF 119

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV-----RRPTDYNPT 262
               +A +AM A+DG + +G  +RV      RP D + +
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSHHS 158

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 65.2 bits (160), Expect = 9e-14
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++ +K +  ++A
Sbjct: 61  -HFHEINNKMVECKKA 75

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 67.1 bits (164), Expect = 1e-13
 Identities = 20/74 (27%), Positives = 34/74 (45%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
             ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A  
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 355 ALNGLKMGDKTLTV 368
            +NG ++ D+ +  
Sbjct: 100 YINGTRLDDRIIRT 113

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 46.3 bits (110), Expect = 2e-06
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 19/93 (20%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---- 223
           ++  + +  +YVG L     E+ I   FS+         +G    +  + +  +K     
Sbjct: 33  EKLLKKSCTLYVGNLSFYTTEEQIYELFSK---------SGD---IKKIIMGLDKMKKTA 80

Query: 224 --FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             F FVE  +  +A NAM  ++G   +   +R 
Sbjct: 81  CGFCFVEYYSRADAENAMRYINGTRLDDRIIRT 113

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 1/84 (1%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
           G+ G   +F+G L     E  + +   +FG  L    +++D DTGNSKGY F  +     
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
           +D A  A+NG  + ++ +TV  A 
Sbjct: 61  SDAAIEAMNGQYLCNRPITVSYAF 84

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 40.6 bits (96), Expect = 6e-05
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            +++G L P  +E+ +   FS       G        + +    + K +AF+   + + +
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61

Query: 236 SNAM-ALDGIIFEGVAVRV 253
             A+ A++G       + V
Sbjct: 62  DAAIEAMNGQYLCNRPITV 80

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 65.1 bits (159), Expect = 2e-13
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 8/91 (8%)

Query: 290 GAEGPDR-VFVGGLPYY------FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCV 342
           G  G D+ + V G P          +  +  L    G +   +   D  TG +KG+ F  
Sbjct: 1   GPLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVE 60

Query: 343 YQDPAVTDIACAALNGLKMGDK-TLTVRRAT 372
                       + +G ++  K  L +    
Sbjct: 61  CGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
               P R+ V  +P+ F +  ++++   FG +   +++ +     SKG+GF  +++ A  
Sbjct: 25  NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADA 82

Query: 350 DIACAALNGLKMGDKTLTVRRATA 373
           D A   L+G  +  + + V  ATA
Sbjct: 83  DRAREKLHGTVVEGRKIEVNNATA 106

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 17/93 (18%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHE 221
           M  +     +R++V  +P    +  +   F Q          G    +++V I       
Sbjct: 21  MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQ---------FGK---ILDVEIIFNERGS 68

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           K F FV      +A  A   L G + EG  + V
Sbjct: 69  KGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 64.0 bits (157), Expect = 2e-13
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++  KT+  + A
Sbjct: 62  -SRHELDSKTIDPKVA 76

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 65.9 bits (161), Expect = 3e-13
 Identities = 20/84 (23%), Positives = 38/84 (45%)

Query: 289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAV 348
              EG   + V  L Y  +   ++ + E +G +    + +DR T  S+G+ F  + D   
Sbjct: 42  PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101

Query: 349 TDIACAALNGLKMGDKTLTVRRAT 372
            + A  A++G  +  + L V+ A 
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMAR 125

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 45.1 bits (107), Expect = 5e-06
 Identities = 24/97 (24%), Positives = 37/97 (38%), Gaps = 24/97 (24%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFV 227
              + V  L    +   +   F +          G    V +VYI  ++       FAFV
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKY---------GR---VGDVYIPRDRYTKESRGFAFV 94

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV-----RRPTD 258
                 +A +AM A+DG + +G  +RV      RP D
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.8 bits (158), Expect = 3e-13
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 4/82 (4%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIA 352
            R+F+GG+P      +I E +      +    +     D   ++G+ F  Y+      +A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 353 CAALN--GLKMGDKTLTVRRAT 372
              L    +++    + V  A 
Sbjct: 69  RRKLMPGRIQLWGHQIAVDWAE 90

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 21/91 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 227
            R+++GG+P +   + I    ++V            + V++V +          + FAFV
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKV-----------TEGVLDVIVYASAADKMKNRGFAFV 57

Query: 228 EMRTVEEASNA---MALDGIIFEGVAVRVRR 255
           E  +   A+ A   +    I   G  + V  
Sbjct: 58  EYESHRAAAMARRKLMPGRIQLWGHQIAVDW 88

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 63.7 bits (156), Expect = 3e-13
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 9/80 (11%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 356 ----LNGLKMGDKTLTVRRA 371
               +           ++ A
Sbjct: 61  KYHNVGL-----SKCEIKVA 75

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           VF   L        +++   + G +    ++ DR++  SKG  +  + +     +A   L
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86

Query: 357 NGLKMGDKTLTVRRATA 373
            G ++    + V+ + A
Sbjct: 87  TGQRLLGVPIIVQASQA 103

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 23/94 (24%), Positives = 33/94 (35%), Gaps = 18/94 (19%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHE 221
               R AR V+   L      + +  FFS V         G    V +V I         
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAV---------GK---VRDVRIISDRNSRRS 66

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 67  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 100

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 64.6 bits (158), Expect = 3e-13
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV GL    TE  +KE    F       +V DR+TG+SKG+GF  +        A  A
Sbjct: 17  TLFVKGLSEDTTEETLKES---FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 356 LNGLKMGDKTLTVRRAT 372
           +   ++    +T+  A 
Sbjct: 74  MEDGEIDGNKVTLDWAK 90

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 22/93 (23%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAI------GGNSAGPGDAVVNVYINHE 221
              ++ ++ ++V GL     E+ +   F   + A        G+S G             
Sbjct: 9   NARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKG------------- 55

Query: 222 KKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             F FV+  + E+A  A  A++    +G  V +
Sbjct: 56  --FGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 67.3 bits (164), Expect = 4e-13
 Identities = 34/196 (17%), Positives = 58/196 (29%), Gaps = 25/196 (12%)

Query: 177 VYVGGLPPLA-NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           + V  L P     Q++   F        G+       V  V I   KK  A V+M    +
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVY-----GD-------VQRVKILFNKKENALVQMADGNQ 84

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQP------SPNLNLAAVGLASGA 287
           A  AM  L+G    G  +R+      N  L       Q       +  L+      +   
Sbjct: 85  AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
                    + +  +P   +E  +K L  S G +    +   +     +           
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVE 200

Query: 348 VTDIACAALNGLKMGD 363
               A   L+   +G+
Sbjct: 201 EAVQALIDLHNHDLGE 216

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 48.5 bits (115), Expect = 1e-06
 Identities = 18/121 (14%), Positives = 38/121 (31%), Gaps = 13/121 (10%)

Query: 272 PSPNLNLAAVGLASGAIGGAEGPDR-------VFVGGL-PYYFTETQIKELLESFGTLHG 323
              + + + +      +G    P         + V  L P   T   +  L   +G +  
Sbjct: 5   HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64

Query: 324 FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQE 383
             ++ +      K        D     +A + LNG K+  K + +  +   + Q   E +
Sbjct: 65  VKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119

Query: 384 S 384
            
Sbjct: 120 E 120

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 47.3 bits (112), Expect = 3e-06
 Identities = 25/122 (20%), Positives = 45/122 (36%), Gaps = 13/122 (10%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
             +P    E       +G + L  F   P     Q     +  +++  +PP  +E+ +  
Sbjct: 112 VQLPREGQEDQGLTKDYGNSPLHRFK-KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKV 170

Query: 194 FFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAV 251
            FS             G      +   ++K A ++M +VEEA  A+  L    + E   +
Sbjct: 171 LFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 220

Query: 252 RV 253
           RV
Sbjct: 221 RV 222

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 23/107 (21%), Positives = 41/107 (38%), Gaps = 16/107 (14%)

Query: 151 GATQLGAFPLM---PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSA 207
           G+  +G  P +    V  + + A       Y+G +P  A E  +   F            
Sbjct: 1   GSQTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNF--------- 51

Query: 208 GPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             G  +++     EK   F++  T E+A+  + AL    F+G  +R 
Sbjct: 52  --GF-ILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 6/73 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
             ++G +P++ TE  +  L ++FG +  F    +      KG  F  Y       +   A
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVA 82

Query: 356 LNGLKMGDKTLTV 368
           L       + L  
Sbjct: 83  LANFPFQGRNLRT 95

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D   A 
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
            +  ++  KT+  + A     Q K
Sbjct: 87  -SRHELDSKTIDPKVAFPRRAQPK 109

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 63.4 bits (155), Expect = 6e-13
 Identities = 19/88 (21%), Positives = 44/88 (50%), Gaps = 4/88 (4%)

Query: 287 AIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
            I  ++  +   ++FVGGL +  ++  +K+    FG +    +  D +TG S+G+GF ++
Sbjct: 1   GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +D A  +         ++  + +  ++A
Sbjct: 61  KDAASVEKVLDQKEH-RLDGRVIDPKKA 87

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 63.2 bits (154), Expect = 7e-13
 Identities = 14/86 (16%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +        +K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRATASS 375
             A    +      K L V+     +
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDA 79

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 51.3 bits (123), Expect = 9e-09
 Identities = 24/105 (22%), Positives = 38/105 (36%), Gaps = 21/105 (20%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           +  +  + V  LP  +N Q +                     +   Y++  K+ AFV + 
Sbjct: 2   SSGSSGILVKNLPQDSNCQEVHDLLKDY-------------DLKYCYVDRNKRTAFVTLL 48

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQPS 273
             E+A NA+       F G  + V+  PTD      A L  G  S
Sbjct: 49  NGEQAQNAIQMFHQYSFRGKDLIVQLQPTD------ALLCSGPSS 87

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 65.3 bits (159), Expect = 9e-13
 Identities = 35/162 (21%), Positives = 57/162 (35%), Gaps = 18/162 (11%)

Query: 239 MALDGIIFE---------GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIG 289
           M+LD II           G   R  RP              +P P  +     L     G
Sbjct: 21  MSLDDIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCG 80

Query: 290 GAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
           G EG +   ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  
Sbjct: 81  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 139

Query: 347 AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQ 388
           A    A     G+ +  + + ++        S+ + E     
Sbjct: 140 ADALKAMKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHHH 176

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 63.1 bits (154), Expect = 9e-13
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E P   +VG LP+   +  I  + +         LV+D+DT   KG+ +  + +      
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLSIR-SVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A    +G  +GD++L V  A 
Sbjct: 72  A-LTYDGALLGDRSLRVDIAE 91

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 19/85 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK------FAFVE 228
              YVG LP    +  I   F  +              + +V +  +K       F +VE
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-------------IRSVRLVRDKDTDKFKGFCYVE 62

Query: 229 MRTVEEASNAMALDGIIFEGVAVRV 253
              V+    A+  DG +    ++RV
Sbjct: 63  FDEVDSLKEALTYDGALLGDRSLRV 87

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 63.1 bits (154), Expect = 1e-12
 Identities = 22/92 (23%), Positives = 41/92 (44%), Gaps = 2/92 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCV 342
           +SG +   +   ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  
Sbjct: 5   SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 343 YQDPAVTDIACAAL-NGLKMGDKTLTVRRATA 373
           +        A  AL +   +  + L +  A +
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 16/88 (18%), Positives = 29/88 (32%), Gaps = 21/88 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFV 227
            ++ V  +P  AN++ I   FS           G    +  V +          + F FV
Sbjct: 16  SKILVRNIPFQANQREIRELFSTF---------GE---LKTVRLPKKMTGTGAHRGFGFV 63

Query: 228 EMRTVEEASNAMA--LDGIIFEGVAVRV 253
           +  T ++A  A           G  + +
Sbjct: 64  DFITKQDAKKAFNALCHSTHLYGRRLVL 91

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 66.3 bits (161), Expect = 1e-12
 Identities = 19/138 (13%), Positives = 41/138 (29%), Gaps = 2/138 (1%)

Query: 257 TDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLE 316
               P     +    P+   ++      +           +++G L ++ T+  + E + 
Sbjct: 31  NGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVH 90

Query: 317 SFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS 374
           S G     +    ++R  G SKG+        A +      L   ++  +   V      
Sbjct: 91  SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

Query: 375 SGQSKTEQESILAQAQQH 392
                  Q     Q+ Q 
Sbjct: 151 FLSQFEMQSRKTTQSGQM 168

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 51.3 bits (122), Expect = 1e-07
 Identities = 25/180 (13%), Positives = 40/180 (22%), Gaps = 17/180 (9%)

Query: 134 PGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIAT 193
                  PE    M     T            +    T     +Y+G L     ++ +  
Sbjct: 28  SANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTE 87

Query: 194 FFSQVMTAIGGNSAGPGDAV-VNVYINHE----KKFAFVEMRTVEEASNAM-ALDGIIFE 247
                         G  D + +  + N      K FA V + +   +   M  L      
Sbjct: 88  AVHS---------LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELH 138

Query: 248 GVAVRVR--RPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY 305
           G    V        +     +    Q          G   G+   A        G  P  
Sbjct: 139 GQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGA 198

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 4/101 (3%)

Query: 282 GLASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY 338
           G +  +     G D    +FVGGL +  T+  ++     +G +    ++KD+ T  S+G+
Sbjct: 1   GSSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGF 60

Query: 339 GFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
           GF  ++DP       A+     +  + +  +  T    Q  
Sbjct: 61  GFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPS 100

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 6/86 (6%)

Query: 295 DRVFVGGLPYYFTETQIKELLESFGTLHGFD--LVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           D + +  +  +     I   L  + +L   +  L+KD+ T  ++G+ F            
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 353 CAALNG----LKMGDKTLTVRRATAS 374
              L      LK+  KT+ V  A ++
Sbjct: 70  LQILQSLHPPLKIDGKTIGVDFAKSA 95

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 46.5 bits (111), Expect = 6e-07
 Identities = 17/99 (17%), Positives = 32/99 (32%), Gaps = 21/99 (21%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------N 219
           M      H   + +  + P     +I T  S                V N+ +       
Sbjct: 1   MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPY---------ASLA-VNNIRLIKDKQTQ 50

Query: 220 HEKKFAFVEMRTVEEASNAM-ALDG----IIFEGVAVRV 253
             + FAFV++ +  +AS  +  L      +  +G  + V
Sbjct: 51  QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 60.7 bits (148), Expect = 6e-12
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           +  P  +F+G L    +  ++K  +      +    V D  TG ++ +G+  ++     +
Sbjct: 14  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 351 IACAALNGLKMGDKTLTVRRATA 373
            A   L GLK+    + + +   
Sbjct: 73  KA-LELTGLKVFGNEIKLEKPKG 94

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ---VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
            +++G L P  +   +    S+                  VV+V     +KF +V+  + 
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLA----------VVDVRTGTNRKFGYVDFESA 68

Query: 233 EEASNAMALDGIIFEGVAVRVRRPT 257
           E+   A+ L G+   G  +++ +P 
Sbjct: 69  EDLEKALELTGLKVFGNEIKLEKPK 93

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 61.1 bits (149), Expect = 8e-12
 Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A AA
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88

Query: 356 LNGLKMGDKTLTVRRATA 373
                +  + +  +RA A
Sbjct: 89  -RPHSIDGRVVEPKRAVA 105

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 60.7 bits (148), Expect = 9e-12
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 1/80 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           + P  +++  LP    E +++ +L+ FG +    +++D  +G S+G GF   +     + 
Sbjct: 23  QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEA 81

Query: 352 ACAALNGLKMGDKTLTVRRA 371
                NG  +          
Sbjct: 82  VIGHFNGKFIKTPPGVSAPT 101

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.5 bits (98), Expect = 5e-05
 Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 24/97 (24%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVY 217
           M +Q  +    +Y+  LP   +EQ +              ++    G S G         
Sbjct: 17  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG--------- 67

Query: 218 INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
                   F  M + E+    +   +G   +      
Sbjct: 68  ------VGFARMESTEKCEAVIGHFNGKFIKTPPGVS 98

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 13/92 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++      R++VG LPP   E+ +   F +     G            V+I+ +K F F+
Sbjct: 9   EKTFTQRSRLFVGNLPPDITEEEMRKLFEK----YG--------KAGEVFIHKDKGFGFI 56

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
            + T   A  A   LD +   G  +RVR    
Sbjct: 57  RLETRTLAEIAKVELDNMPLRGKQLRVRFACH 88

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 58.4 bits (142), Expect = 4e-11
 Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 9/95 (9%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ GG +      R+FVG LP   TE ++++L E +G      + KD      KG+GF
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGF 55

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
              +   + +IA   L+ + +  K L VR A  S+
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 90

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 60.5 bits (147), Expect = 1e-11
 Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 10/90 (11%)

Query: 291 AEGPDR-VFVGGLPYYFTE------TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           A+G D  + V  +P    +        I ++   FG +   +     + G +KGY F  Y
Sbjct: 11  ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEY 68

Query: 344 QDPAVTDIACAALNGLKMGDK-TLTVRRAT 372
             PA    A    +G K+  + T  V   T
Sbjct: 69  ASPAHAVDAVKNADGYKLDKQHTFRVNLFT 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 43.6 bits (103), Expect = 9e-06
 Identities = 19/97 (19%), Positives = 34/97 (35%), Gaps = 24/97 (24%)

Query: 175 RRVYVGGLPPLANEQ------AIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKF 224
             + V  +P +  ++       I   FS+          G    + N +   E    K +
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF---------GK---ITNDFYPEEDGKTKGY 63

Query: 225 AFVEMRTVEEASNAM-ALDGIIFEG-VAVRVRRPTDY 259
            F+E  +   A +A+   DG   +     RV   TD+
Sbjct: 64  IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDF 100

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 60.0 bits (146), Expect = 1e-11
 Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 4/91 (4%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+        ++FVG L    +E  +  L + FG +    +++  D G+SKG  F  +
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKF 63

Query: 344 QDPAVTDIACAALNG---LKMGDKTLTVRRA 371
                   A  AL+G   +     +L V+ A
Sbjct: 64  SSHTEAQAAIHALHGSQTMPGASSSLVVKFA 94

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 25/84 (29%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           R+++VG L    +E+ +   F          V+    G+S G                AF
Sbjct: 16  RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG---------------CAF 60

Query: 227 VEMRTVEEASNAM-ALDG-IIFEG 248
           V+  +  EA  A+ AL G     G
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPG 84

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  ++F+G LP   TE +I+ L E +G +   D++        K YGF   +D    
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
           + A   L+  K+    + V  +   S  S 
Sbjct: 56  EDAIRNLHHYKLHGVNINVEASKNKSKASS 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 21/80 (26%), Positives = 32/80 (40%), Gaps = 15/80 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            ++++G LP  A EQ I + F Q          G    V+   I   K + FV +     
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQY---------GK---VLECDI--IKNYGFVHIEDKTA 54

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+  L      GV + V
Sbjct: 55  AEDAIRNLHHYKLHGVNINV 74

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.4 bits (144), Expect = 2e-11
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 3/85 (3%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG++   +   ++ +  +P +     +  LL  +G +   + V               Y
Sbjct: 5   SSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTY 61

Query: 344 QDPAVTDIACAALNGLKMGDKTLTV 368
                   A   LNG ++ + TL V
Sbjct: 62  SSKDQARQALDKLNGFQLENFTLKV 86

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 51.3 bits (123), Expect = 1e-08
 Identities = 15/89 (16%), Positives = 33/89 (37%), Gaps = 10/89 (11%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
            +  R++ +  +PP    + + +   Q          G  ++   V  + E     V   
Sbjct: 12  RQRIRKLQIRNIPPHLQWEVLDSLLVQ---------YGVVESCEQVNTDSETAVVNVTYS 62

Query: 231 TVEEASNAM-ALDGIIFEGVAVRVRRPTD 258
           + ++A  A+  L+G   E   ++V    D
Sbjct: 63  SKDQARQALDKLNGFQLENFTLKVAYIPD 91

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.7 bits (145), Expect = 2e-11
 Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 13/95 (13%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
           +  + +  Q++     VY GG+     +Q +   FS      G         ++ + +  
Sbjct: 12  LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSP----FG--------QIMEIRVFP 59

Query: 221 EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           EK ++FV   T E A++A+ +++G   EG  V+  
Sbjct: 60  EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.6 bits (124), Expect = 2e-08
 Identities = 14/84 (16%), Positives = 29/84 (34%), Gaps = 6/84 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ GG+    T+  +++    FG +    +  +      KGY F  +        A  +
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80

Query: 356 LNGLKMGDKTLTVRRATASSGQSK 379
           +NG  +    +       S   + 
Sbjct: 81  VNGTTIEGHVVKCYWGKESPDMTS 104

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 10/89 (11%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  L     + ++++    FGT+    ++   + G SKG+GF  +  P     A   
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74

Query: 356 LNGLKMGDKTLTV--------RRATASSG 376
           +NG  +  K L V        R++  SSG
Sbjct: 75  MNGRIVATKPLYVALAQRKEERQSGPSSG 103

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 21/87 (24%), Positives = 32/87 (36%), Gaps = 25/87 (28%)

Query: 176 RVYVGGLPPLANEQAIATFFSQ--------VMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
            +YV  L    +++ +   FS         VM   GG S G               F FV
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKG---------------FGFV 60

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
              + EEA+ A+  ++G I     + V
Sbjct: 61  CFSSPEEATKAVTEMNGRIVATKPLYV 87

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 21/89 (23%), Positives = 34/89 (38%), Gaps = 13/89 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK-KFAF 226
              +   R V+V G P   +   ++ +F            GP   V +V ++ +K  FA 
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLA---------FGP---VASVVMDKDKGVFAI 49

Query: 227 VEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           VEM  V      ++       G  +RVR 
Sbjct: 50  VEMGDVGAREAVLSQSQHSLGGHRLRVRP 78

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 6/93 (6%)

Query: 287 AIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP 346
              G+ G   VFV G P      Q+ E   +FG +    +V D+D G    +      D 
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKG---VFAIVEMGDV 55

Query: 347 AVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
              +    + +   +G   L VR       QS 
Sbjct: 56  GAREAVL-SQSQHSLGGHRLRVRPREQKEFQSP 87

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 14/90 (15%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           +    +    +YVGGL     E  +   F Q            G+ +  + +   ++ AF
Sbjct: 5   SSGEDKTITTLYVGGLGDTITETDLRNHFYQ-----------FGE-IRTITVVQRQQCAF 52

Query: 227 VEMRTVEEASNAM--ALDGIIFEGVAVRVR 254
           ++  T + A  A   + + +I  G  + V+
Sbjct: 53  IQFATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA-CAA 355
           ++VGGL    TET ++     FG +    +V+       +   F  +      ++A   +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68

Query: 356 LNGLKMGDKTLTVR 369
            N L +  + L V+
Sbjct: 69  FNKLIVNGRRLNVK 82

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 57.3 bits (139), Expect = 1e-10
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTD 350
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 13  SPPYTAFLGNLPYDVTEESIKEFFRGLNISA-VRLPREPSNPERLKGFGYAEFEDLD-SL 70

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           ++  +LN   +G+K + V  A 
Sbjct: 71  LSALSLNEESLGNKRIRVDVAD 92

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 53.0 bits (128), Expect = 4e-09
 Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 20/87 (22%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 227
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 62

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVR 254
           E   ++   +A++L+        +RV 
Sbjct: 63  EFEDLDSLLSALSLNEESLGNKRIRVD 89

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 7/90 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G +    + K       + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNS 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 14/89 (15%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVE 228
            +  +  V+VG       E  +  FFSQ      G+       V++V+I    + FAFV 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQY-----GD-------VMDVFIPKPFRAFAFVT 48

Query: 229 MRTVEEASNAMALDGIIFEGVAVRVRRPT 257
               + A +    D II +G++V +    
Sbjct: 49  FADDQIAQSLCGEDLII-KGISVHISNAE 76

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 8/93 (8%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G+ G +    ++FVG +    T  +++ L E  G +   D+V        K Y F   + 
Sbjct: 1   GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEK 52

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
            A    A A LNG ++  K + V  +T    +S
Sbjct: 53  EADAKAAIAQLNGKEVKGKRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 51.8 bits (125), Expect = 6e-09
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 15/84 (17%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
           + +  +++VG +      Q + + F +          G    V+   +   K +AFV M 
Sbjct: 6   SGNTWKIFVGNVSAACTSQELRSLFER---------RGR---VIECDV--VKDYAFVHME 51

Query: 231 TVEEASNAM-ALDGIIFEGVAVRV 253
              +A  A+  L+G   +G  + V
Sbjct: 52  KEADAKAAIAQLNGKEVKGKRINV 75

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTD 350
             P   F+G LPY  TE  IKE            L ++  +    KG+G+  ++D   + 
Sbjct: 17  SPPYTAFLGNLPYDVTEESIKEFFRGLNIS-AVRLPREPSNPERLKGFGYAEFEDLD-SL 74

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           ++  +LN   +G++ + V  A 
Sbjct: 75  LSALSLNEESLGNRRIRVDVAD 96

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 20/86 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-------FAFV 227
              ++G LP    E++I  FF  +              +  V +  E         F + 
Sbjct: 20  YTAFLGNLPYDVTEESIKEFFRGL-------------NISAVRLPREPSNPERLKGFGYA 66

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRV 253
           E   ++   +A++L+        +RV
Sbjct: 67  EFEDLDSLLSALSLNEESLGNRRIRV 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 5/76 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VG LP     + +K  L   G++              +   F  Y D A    A + 
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSAAAQQAVSC 75

Query: 356 LNGLKMGDKTLTVRRA 371
           L GL++G  TL V  A
Sbjct: 76  LQGLRLGTDTLRVALA 91

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 12/87 (13%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           +    A  VYVG LP  A    +     ++           G   + +     ++ AF+ 
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALREL-----------GSVPLRLTWQGPRRRAFLH 62

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVR 254
                 A  A+  L G+      +RV 
Sbjct: 63  YPDSAAAQQAVSCLQGLRLGTDTLRVA 89

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VGGL P  +  A+A  F +     G        ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDR----FG--------SIRTIDHVKGDSFAYIQYESLDA 65

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A   + G    G   R+R
Sbjct: 66  AQAACAKMRGFPLGGPDRRLR 86

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 6/74 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R++VGGL    +   +    + FG++   D VK         + +  Y+       ACA 
Sbjct: 19  RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAACAK 72

Query: 356 LNGLKMGDKTLTVR 369
           + G  +G     +R
Sbjct: 73  MRGFPLGGPDRRLR 86

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.6 bits (137), Expect = 3e-10
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 13/106 (12%)

Query: 284 ASGAIGGAEGPD----------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG 333
           +SG+ G + G            R++VG LP       I+++   +G +   DL   R   
Sbjct: 2   SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR--- 58

Query: 334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
               + F  ++DP   + A    +G       L V    +  G   
Sbjct: 59  GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 10/85 (11%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A  +  R+YVG LPP    + I   F +          G    +          FAFVE 
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYK---------YGAIRDIDLKNRRGGPPFAFVEF 68

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
               +A +A+   DG  ++G  +RV
Sbjct: 69  EDPRDAEDAVYGRDGYDYDGYRLRV 93

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.3 bits (136), Expect = 3e-10
 Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 17/96 (17%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKF-- 224
           +     R VY+ G P  A    I  +             G    V+N+ +     K F  
Sbjct: 6   KNDVKNRSVYIKGFPTDATLDDIKEWLEDK---------GQ---VLNIQMRRTLHKAFKG 53

Query: 225 -AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPTDY 259
             FV   ++E A   +   G  ++   + +    DY
Sbjct: 54  SIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 6/89 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ G P   T   IKE LE  G +    + +       KG  F V+      + A   +
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSI---ESAKKFV 69

Query: 357 --NGLKMGDKTLTVRRATASSGQSKTEQE 383
              G K  +  L +        +   E++
Sbjct: 70  ETPGQKYKETDLLILFKDDYFAKKNEERK 98

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.1 bits (133), Expect = 4e-10
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 9/79 (11%)

Query: 297 VFVGGLP------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTD 350
           + V  +P          +  I ++   FG +   +     + G +KGY F  Y  PA   
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAHAV 61

Query: 351 IACAALNGLKMGDK-TLTV 368
            A    +G K+  + T  V
Sbjct: 62  DAVKNADGYKLDKQHTFRV 80

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 23/83 (27%)

Query: 177 VYVGGLPPLANEQ------AIATFFSQVMTAIGGNSAGPGDAVVNVYINHE----KKFAF 226
           + V  +P +  ++       I   FS+          G    + N +   E    K + F
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKF---------GK---ITNDFYPEEDGKTKGYIF 51

Query: 227 VEMRTVEEASNAM-ALDGIIFEG 248
           +E  +   A +A+   DG   + 
Sbjct: 52  LEYASPAHAVDAVKNADGYKLDK 74

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 15/99 (15%), Positives = 32/99 (32%), Gaps = 15/99 (15%)

Query: 289 GGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G          VFVG      T  ++++    +G +    + K       + + F  + D
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             V    C     L +   ++ +  A     + K  + +
Sbjct: 58  DKVAQSLCG--EDLIIKGISVHISNA-----EPKHNKLN 89

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 14/89 (15%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAF 226
                H  +V+VG        + +  FF Q      G        VV+V+I    + FAF
Sbjct: 5   HHHHHHGSKVFVGRCTEDMTAEELQQFFCQY-----GE-------VVDVFIPKPFRAFAF 52

Query: 227 VEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           V     + A +    D II +G++V +  
Sbjct: 53  VTFADDKVAQSLCGEDLII-KGISVHISN 80

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 55.5 bits (134), Expect = 6e-10
 Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 1/94 (1%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG            +  +P+  T+  + + LE          V   + G   G     ++
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFK 65

Query: 345 DPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
           +      +   L+  K+  +   V   T    + 
Sbjct: 66  NEDDARKS-ERLHRKKLNGREAFVHVVTLEDMRE 98

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 50.1 bits (120), Expect = 4e-08
 Identities = 14/112 (12%), Positives = 33/112 (29%), Gaps = 14/112 (12%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FA 225
                    ++  +P    +  +  F   +            +  V+V +++  +    A
Sbjct: 10  DVNSAKVCAHITNIPFSITKMDVLQFLEGI---------PVDENAVHVLVDNNGQGLGQA 60

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRRPT--DYNPTLAAALGPGQPSPN 275
            V+ +  ++A  +  L      G    V   T  D           G+  P+
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPS 112

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 59.1 bits (142), Expect = 1e-09
 Identities = 17/79 (21%), Positives = 35/79 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +FV  + Y  TE++++   E +G +    +V  + +G  +GY F  Y+       A    
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 357 NGLKMGDKTLTVRRATASS 375
           +G K+  + + V      +
Sbjct: 165 DGKKIDGRRVLVDVERGRT 183

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 57.6 bits (138), Expect = 3e-09
 Identities = 18/89 (20%), Positives = 27/89 (30%)

Query: 23  SGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRH 82
             R R+ ++ RDR  R  +S    RR  +  +  R G  D        D   D       
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGEL 335

Query: 83  RSRSHSSDRFRNRSKSLSPSRSPSKSKRR 111
                     + R +     RS    + R
Sbjct: 336 GPDGPDGPEEKGRDRDRERRRSHRSERER 364

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 56.0 bits (134), Expect = 1e-08
 Identities = 14/88 (15%), Positives = 25/88 (28%)

Query: 25  RSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYNRDKERRHRHRS 84
           R R   R R+R  R+ +   + R    +     E            +   D       + 
Sbjct: 288 RKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKG 347

Query: 85  RSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           R    +R R+        R   + + R 
Sbjct: 348 RDRDRERRRSHRSERERRRDRDRDRDRD 375

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 55.6 bits (133), Expect = 1e-08
 Identities = 17/106 (16%), Positives = 28/106 (26%)

Query: 7   RYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRT 66
           R  +     R +S     R R+ ER +D+     +     R R +  +  +E +R     
Sbjct: 256 RSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGD 315

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
                   D                     K     R   +S R  
Sbjct: 316 MAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSE 361

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 55.6 bits (133), Expect = 1e-08
 Identities = 21/114 (18%), Positives = 33/114 (28%), Gaps = 1/114 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                   A    +             G  G D      +    +RRR    + +R   R
Sbjct: 309 LRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDR 368

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFD 115
           D DR DR R++ R +    R R  +      ++       + S        G D
Sbjct: 369 DRDR-DRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGD 421

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 55.2 bits (132), Expect = 2e-08
 Identities = 17/112 (15%), Positives = 30/112 (26%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
              R  R       SR +      RSR   + +DR  +   S   +R R +  + +    
Sbjct: 252 RERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRG 311

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              D  +     +   +            D    + +     R  S    R 
Sbjct: 312 GGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERE 363

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.5 bits (130), Expect = 3e-08
 Identities = 10/112 (8%), Positives = 19/112 (16%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
                 R                      +  R R     K    DR+R  +   +R   
Sbjct: 242 RERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARR 301

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
               + +         E      +                      + + R 
Sbjct: 302 ERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRE 353

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.5 bits (130), Expect = 3e-08
 Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 1/111 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             R+ + +  G G        +G +   +        D   G +++ RD++ +  R    
Sbjct: 301 RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           + +R  R RD +RD++R H+   R     R   R                S
Sbjct: 361 ERER-RRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDS 410

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.1 bits (129), Expect = 4e-08
 Identities = 19/116 (16%), Positives = 34/116 (29%), Gaps = 5/116 (4%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
           S    R     E            +   E G                 D   +  R+  R
Sbjct: 293 SRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDR 352

Query: 62  DHDR-----TDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           +  R      +R RD +RD++R   H+     S+R R+ ++     +        +
Sbjct: 353 ERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGN 408

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 54.1 bits (129), Expect = 4e-08
 Identities = 16/111 (14%), Positives = 28/111 (25%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                R        + +SS    R+R     ++          +          D     
Sbjct: 275 RRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGE 334

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
                    +       R R RS     +R R+R +     R   + +R S
Sbjct: 335 LGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGS 385

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 53.3 bits (127), Expect = 8e-08
 Identities = 9/112 (8%), Positives = 23/112 (20%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                R  +     R +S       R   R R +     +     R R++  +       
Sbjct: 249 DKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEE 308

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
                    + +   +                +  +     R   + +    
Sbjct: 309 LRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRS 360

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 52.9 bits (126), Expect = 9e-08
 Identities = 13/106 (12%), Positives = 30/106 (28%)

Query: 7   RYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRT 66
           R     +    + S    + +  +R R       ++  +  R+++      +     +  
Sbjct: 264 RRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

Query: 67  DRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           D   D     E             R R+R +  S      + + R 
Sbjct: 324 DAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRD 369

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 11/113 (9%), Positives = 20/113 (17%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
                 R          +    S       R R+R     +       R +         
Sbjct: 246 RERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERER 305

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           ++  R          +                          R   + +RRS 
Sbjct: 306 KEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSH 358

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 52.2 bits (124), Expect = 2e-07
 Identities = 20/112 (17%), Positives = 28/112 (25%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             R  R  +  +    K      R R       +       G      +       +G  
Sbjct: 273 ERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPP 332

Query: 62  DHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
                D           R R R RSH S+R R R +     R     +   G
Sbjct: 333 GELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERG 384

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.8 bits (123), Expect = 3e-07
 Identities = 20/119 (16%), Positives = 33/119 (27%), Gaps = 3/119 (2%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
                                        R RDR  R       +RRRD++   DR+  R
Sbjct: 319 PSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRD--R 376

Query: 62  DHDRTDRHRDYNRDKE-RRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFDMAPP 119
           +H R +R  +  RD+       +          +R   +            +G+ M   
Sbjct: 377 EHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMYMESEGGDGYLAPENGYLMEAA 435

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.4 bits (122), Expect = 3e-07
 Identities = 17/109 (15%), Positives = 26/109 (23%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           +D   D     SR +      R R  E           S   D   D     +       
Sbjct: 282 KDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPD 341

Query: 64  DRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              ++ RD +R++ R HR                           + R 
Sbjct: 342 GPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRD 390

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 51.0 bits (121), Expect = 4e-07
 Identities = 16/112 (14%), Positives = 26/112 (23%), Gaps = 3/112 (2%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
              RD   +               RSR+ +R R    RD +     R R K+   DR   
Sbjct: 232 DRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDR--- 288

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           +      R R     + +          ++                      
Sbjct: 289 KRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 50.6 bits (120), Expect = 5e-07
 Identities = 31/110 (28%), Positives = 40/110 (36%)

Query: 3   GRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRD 62
           G       V      +        R G        RD     + R R +    +RE  R 
Sbjct: 198 GTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRS 257

Query: 63  HDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
             R  R R  +RDKE R R R RS   DR R R  S S  R+  + +R+ 
Sbjct: 258 RSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKE 307

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 50.2 bits (119), Expect = 8e-07
 Identities = 19/115 (16%), Positives = 28/115 (24%), Gaps = 5/115 (4%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
           R  R        R +   + G         +        G              E  RD 
Sbjct: 291 RSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDR 350

Query: 64  DRTDRHRDYNRDKERRHRHRSR-----SHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           DR  R    +  + RR R R R         +R   R +  +      +     G
Sbjct: 351 DRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEG 405

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.5 bits (117), Expect = 1e-06
 Identities = 18/113 (15%), Positives = 32/113 (28%), Gaps = 3/113 (2%)

Query: 4   RDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDH 63
                D   +  R +      R +  ER R R     +      + ++    +R   +D 
Sbjct: 227 PLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDR 286

Query: 64  DR---TDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           DR   + R R+  R +  R              + +    P   P       G
Sbjct: 287 DRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDG 339

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 49.5 bits (117), Expect = 1e-06
 Identities = 11/112 (9%), Positives = 20/112 (17%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
            S    +               S      ER R R     K     RR  ++ +  R   
Sbjct: 244 RSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRER 303

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
              +          +                           +   + + R 
Sbjct: 304 ERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRERR 355

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 48.7 bits (115), Expect = 2e-06
 Identities = 26/101 (25%), Positives = 44/101 (43%)

Query: 13  EGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDY 72
              RH     + R           HRD     +  RR+++ + D+E  R   R+   R  
Sbjct: 206 VNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRR 265

Query: 73  NRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           +R +++  R RSR  S D+ R+R +  S SR  ++ +R   
Sbjct: 266 SRSRDKEERRRSRERSKDKDRDRKRRSSRSRERARRERERK 306

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 48.7 bits (115), Expect = 2e-06
 Identities = 21/112 (18%), Positives = 32/112 (28%)

Query: 1   MSGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGI 60
            S  D R        R +        R   R RD+     +S   DRRR    +   E  
Sbjct: 216 TSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERR 275

Query: 61  RDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRS 112
           R  +R+       + +  R R R+R     +   R      +          
Sbjct: 276 RSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPP 327

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 48.7 bits (115), Expect = 2e-06
 Identities = 21/115 (18%), Positives = 28/115 (24%), Gaps = 1/115 (0%)

Query: 2   SGRDIRYDAVGEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIR 61
             RD +  +     R +          G  G      +      D         D     
Sbjct: 284 KDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGP 343

Query: 62  DHDRTDRHRDYNRDKER-RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSGFD 115
           +    DR R+  R     R R R R    DR R   +    S       R  G  
Sbjct: 344 EEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGG 398

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 48.3 bits (114), Expect = 3e-06
 Identities = 25/103 (24%), Positives = 37/103 (35%), Gaps = 1/103 (0%)

Query: 12  GEGSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRD 71
               R   S +  R R  +R R+R  R  +   +  RR    +  R   R  D+ +R R 
Sbjct: 218 RYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRS 277

Query: 72  YNRDKER-RHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
             R K++ R R R  S S +R R   +     R          
Sbjct: 278 RERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPS 320

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 20/100 (20%), Positives = 32/100 (32%)

Query: 14  GSRHKSSWVSGRSRTGERGRDRHHRDFKSGGDDRRRDKNYKYDREGIRDHDRTDRHRDYN 73
           G          R R  ER      RD +      R     +  R   ++  R  R R  +
Sbjct: 224 GPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKD 283

Query: 74  RDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRRSG 113
           +D++R+ R       + R R R + L            +G
Sbjct: 284 KDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAG 323

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 15/85 (17%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           + + + +++VG + P    Q +   F +          GP   V+   I   K +AFV M
Sbjct: 6   SGKASTKLHVGNISPTCTNQELRAKFEE---------YGP---VIECDI--VKDYAFVHM 51

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV 253
              E+A  A+  LD   F+G  + V
Sbjct: 52  ERAEDAVEAIRGLDNTEFQGKRMHV 76

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 52.6 bits (127), Expect = 4e-09
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +   ++ VG +    T  +++   E +G +   D+V        K Y F   +       
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVE 59

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A   L+  +   K + V+ +T
Sbjct: 60  AIRGLDNTEFQGKRMHVQLST 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 5/83 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L     + +++     +G L    + ++       G+ F  ++DP   + A   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           L+G  +    + V  +T    +S
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRS 79

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 49.6 bits (119), Expect = 6e-08
 Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 14/80 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEE 234
           +VYVG L   A +  +   FS           GP   +  V+I      FAFVE     +
Sbjct: 2   KVYVGNLGTGAGKGELERAFSY---------YGP---LRTVWIARNPPGFAFVEFEDPRD 49

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A +A+  LDG +  G  VRV
Sbjct: 50  AEDAVRGLDGKVICGSRVRV 69

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 53.7 bits (129), Expect = 3e-09
 Identities = 15/93 (16%), Positives = 27/93 (29%), Gaps = 10/93 (10%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
                 R+ +  LP   + Q +     +                 +V          +E 
Sbjct: 24  LPAKRYRITMKNLPEGCSWQDLKDLARE---------NSLETTFSSVNTRDFDGTGALEF 74

Query: 230 RTVEEASNAMA-LDGIIFEGVAVRVRRPTDYNP 261
            + E    A+  L+ I F G  + V R  +  P
Sbjct: 75  PSEEILVEALERLNNIEFRGSVITVERDDNPPP 107

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 48.3 bits (115), Expect = 2e-07
 Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+ +  LP   +   +K+L         F      +T +  G G   +    +   A   
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILVEALER 86

Query: 356 LNGLKMGDKTLTVRRAT 372
           LN ++     +TV R  
Sbjct: 87  LNNIEFRGSVITVERDD 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FV   P    E+++ E+   FG +    ++         G+ F  +++      A   
Sbjct: 33  RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84

Query: 356 LNGLKMGDKTLTVRRA 371
           ++G    ++ L V  +
Sbjct: 85  VHGKSFANQPLEVVYS 100

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 21/89 (23%), Positives = 30/89 (33%), Gaps = 15/89 (16%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           Q+      R++V   P    E  +   F            GP   +  V I     FAFV
Sbjct: 25  QEGELSNTRLFVRPFPLDVQESELNEIFGPF---------GP---MKEVKI--LNGFAFV 70

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
           E    E A+ A+  + G  F    + V  
Sbjct: 71  EFEEAESAAKAIEEVHGKSFANQPLEVVY 99

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 53.7 bits (129), Expect = 6e-09
 Identities = 15/85 (17%), Positives = 29/85 (34%), Gaps = 5/85 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 350
           R++V  L  +  E  +K +   +             ++    G  KG  F    +     
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 351 IACAALNGLKMGDKTLTVRRATASS 375
            A    NG  +  K + V+ A ++ 
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSAR 131

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 53.7 bits (129), Expect = 6e-09
 Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 5/76 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +V+VG L     +T+++     +G L    + ++       G+ F  ++DP     A   
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 356 LNGLKMGDKTLTVRRA 371
           L+G  +    + V  +
Sbjct: 130 LDGRTLCGCRVRVELS 145

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 51.4 bits (123), Expect = 4e-08
 Identities = 25/101 (24%), Positives = 39/101 (38%), Gaps = 14/101 (13%)

Query: 155 LGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV 214
           +          M + +     +VYVG L    N+  +   F            GP   + 
Sbjct: 54  VTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYY---------GP---LR 101

Query: 215 NVYINHEKK-FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           +V++      FAFVE     +A++A+  LDG    G  VRV
Sbjct: 102 SVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 13/80 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + +YV  L    +E+ I   F+ +          PG       +   + +AFV     E+
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNI---------KPG---AVERVKKIRDYAFVHFSNRED 63

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A  AM AL+G + +G  + V
Sbjct: 64  AVEAMKALNGKVLDGSPIEV 83

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 51.9 bits (125), Expect = 8e-09
 Identities = 13/75 (17%), Positives = 24/75 (32%), Gaps = 6/75 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++V  L    +E  I++   +                  + Y F  + +      A  AL
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMKAL 71

Query: 357 NGLKMGDKTLTVRRA 371
           NG  +    + V  A
Sbjct: 72  NGKVLDGSPIEVTLA 86

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 16/83 (19%), Positives = 27/83 (32%), Gaps = 6/83 (7%)

Query: 297 VFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNSK---GYGFCVYQDPAVTD 350
           VFV GL     + ++    E    FG +H   +        S+      +  Y       
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 351 IACAALNGLKMGDKTLTVRRATA 373
            A   +N + +  +TL     T 
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTT 100

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 21/88 (23%)

Query: 177 VYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---------FAF 226
           V+V GL   LA+ + +     +     G         +  V IN+             A+
Sbjct: 18  VFVVGLSQRLADPEVLKR--PEYFGKFG--------KIHKVVINNSTSYAGSQGPSASAY 67

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           V     E+A  A+  ++ ++ +G  ++ 
Sbjct: 68  VTYIRSEDALRAIQCVNNVVVDGRTLKA 95

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.9 bits (122), Expect = 2e-08
 Identities = 14/98 (14%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G +        V + GLP+  ++ +I +       +     +     G S G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQS 378
             +    + + A    +  ++G + + + +++ +  ++
Sbjct: 62  VQFASQEIAEKAL-KKHKERIGHRYIEIFKSSRAEVRT 98

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 46.7 bits (111), Expect = 6e-07
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 12/93 (12%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---F 224
              T +   V + GLP   +++ I  FFS +     G         + + ++ + +    
Sbjct: 9   SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG---------MTLPVDFQGRSTGE 59

Query: 225 AFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           AFV+  + E A  A+           + + + +
Sbjct: 60  AFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 50.4 bits (121), Expect = 3e-08
 Identities = 19/109 (17%), Positives = 35/109 (32%), Gaps = 13/109 (11%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
            S    G      +FV  L    TE  +++    FG L     +KD        Y F  +
Sbjct: 1   GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
            +      A   +NG  +  + + +  A     +   ++       +Q 
Sbjct: 53  DERDGAVKAMEEMNGKDLEGENIEIVFA-----KPPDQKRKERKAQRQA 96

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 21/105 (20%), Positives = 35/105 (33%), Gaps = 19/105 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + ++V  L     E+ +   FSQ          G    +  V     K +AF+     + 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQF---------GK---LERVKKL--KDYAFIHFDERDG 57

Query: 235 ASNAM-ALDGIIFEGVAVRV---RRPTDYNPTLAAALGPG-QPSP 274
           A  AM  ++G   EG  + +   + P        A       PS 
Sbjct: 58  AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 50.2 bits (120), Expect = 4e-08
 Identities = 16/100 (16%), Positives = 28/100 (28%), Gaps = 10/100 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E    FG+      +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGS------LGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRA----TASSGQSKTEQESILAQAQQH 392
              K     L +  A      ++ Q K  Q    A+  + 
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 43.6 bits (103), Expect = 1e-05
 Identities = 17/87 (19%), Positives = 24/87 (27%), Gaps = 13/87 (14%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
             + R    +    LP       I   FS+          G    +  V +      A V
Sbjct: 4   GSSGRSKTVILAKNLPAGTLAAEIQETFSR---------FGS---LGRVLLPEGGITAIV 51

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
           E     EA  A   L    F  V + +
Sbjct: 52  EFLEPLEARKAFRHLAYSKFHHVPLYL 78

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 48.9 bits (117), Expect = 1e-07
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 9/83 (10%)

Query: 296 RVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+G L      ++ ++ +   +G + G  +         KGY F  Y +      A  
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80

Query: 355 ALNGLKMGDKTLTVRRATASSGQ 377
             NG  +  +TL +  A      
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 16/82 (19%)

Query: 175 RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            RV++G L   L  +  + T FS+          G    V    ++  K +AFV+     
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSK---------YGR---VAGCSVH--KGYAFVQYSNER 73

Query: 234 EASNAM-ALDGIIFEGVAVRVR 254
            A  A+   +G +  G  + + 
Sbjct: 74  HARAAVLGENGRVLAGQTLDIN 95

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 1/91 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E    V++ GLP+      + +  +    +     +     G + G GF  +++ A    
Sbjct: 23  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 82

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
           A    +   MG++ + V   T      K + 
Sbjct: 83  AL-CRHKQYMGNRFIQVHPITKKGMLEKIDM 112

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 47.1 bits (112), Expect = 7e-07
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 12/84 (14%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFVEMRTVE 233
           VY+ GLP  A  + +  FF ++            +  + +      K     FVE R   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKL---------DIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 234 EASNAMALDGIIFEGVAVRVRRPT 257
           +   A+           ++V   T
Sbjct: 79  DYKAALCRHKQYMGNRFIQVHPIT 102

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 12/78 (15%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V + GLP+  T+ +I +       +     +     G   G  F  +    + + A    
Sbjct: 45  VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103

Query: 357 NGLKMGDKTLTVRRATAS 374
           +  ++G + + V +++  
Sbjct: 104 HKERIGHRYIEVFKSSQE 121

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 46.0 bits (109), Expect = 2e-06
 Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FA 225
              + +   V + GLP    ++ I  FFS +            + +        K    A
Sbjct: 36  SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVP--------NGITLPVDPEGKITGEA 87

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
           FV+  + E A  A+           + V + +
Sbjct: 88  FVQFASQELAEKALGKHKERIGHRYIEVFKSS 119

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 19/106 (17%), Positives = 38/106 (35%), Gaps = 16/106 (15%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V + GLP   + + +  F S              D V  V+  + ++      AFVE+ +
Sbjct: 20  VKLRGLPWSCSIEDVQNFLS---------DCTIHDGVAGVHFIYTREGRQSGEAFVELES 70

Query: 232 VEEASNAMALDGIIFEGVAVRVRR--PTDYNPTLAAALGPGQPSPN 275
            ++   A+  D        + V +   T+ +  L  +       P+
Sbjct: 71  EDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPS 116

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 23/119 (19%), Positives = 46/119 (38%), Gaps = 16/119 (13%)

Query: 284 ASGAIGGAEGPDR-----VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNS 335
           +SG+ G   GP+      V + GLP+  +   ++  L        + G   +  R+ G  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQ 60

Query: 336 KGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIA 394
            G  F   +      +A    +   MG + + V ++       +TE + +L  +  + A
Sbjct: 61  SGEAFVELESEDDVKLAL-KKDRESMGHRYIEVFKS------HRTEMDWVLKHSGPNSA 112

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 47.7 bits (113), Expect = 4e-07
 Identities = 21/71 (29%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 290 GAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD--TGNSKGYGFCVYQ 344
           G+ G      VFVGGLP    E +I      FG L      K         KGY F ++Q
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 345 DPAVTDIACAA 355
           + +       A
Sbjct: 61  EESSVQALIDA 71

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 50.3 bits (119), Expect = 4e-07
 Identities = 15/121 (12%), Positives = 45/121 (37%), Gaps = 7/121 (5%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 11  TIYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 67

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQHIAIQKMALQTSGMNTLGGG 411
           A  ++ G    DK + ++ A   S      + + + + ++    +  + +T        G
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 412 M 412
            
Sbjct: 128 G 128

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.4 bits (109), Expect = 7e-06
 Identities = 28/204 (13%), Positives = 53/204 (25%), Gaps = 13/204 (6%)

Query: 52  NYKYDREGIRDHDRTDRHRDYNRDKERRHRHRSRSHSSDRFRNRSKSLSPSRSPSKSKRR 111
            Y      I    +        + ++R+ + +    +    +    +             
Sbjct: 85  QYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGM 144

Query: 112 SGFDMAPPAAAMLPGAAVPGQLPGVPSAVPEMAQNMLPFGATQLGAFPLMPVQVMTQQAT 171
                AP     +PG       PG+          + P         P            
Sbjct: 145 PPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSEN 204

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
                +++  LP   NE  ++  F+Q                    +      AFVE   
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQF-----------PGFKEVRLVPGRHDIAFVEFDN 253

Query: 232 VEEASNAM-ALDGI-IFEGVAVRV 253
             +A  A  AL G  I +  A+++
Sbjct: 254 EVQAGAARDALQGFKITQNNAMKI 277

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 43.7 bits (102), Expect = 6e-05
 Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 223
           M    TR    +Y+  L     +  +      + +  G         ++++ ++   K  
Sbjct: 1   MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFG--------QILDILVSRSLKMR 52

Query: 224 -FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
             AFV  + V  A+NA+ ++ G  F    +R+
Sbjct: 53  GQAFVIFKEVSSATNALRSMQGFPFYDKPMRI 84

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 24/75 (32%), Gaps = 6/75 (8%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN 357
           F+  LP    E  +  L   F       LV  R         F  + +      A  AL 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

Query: 358 GLKM-GDKTLTVRRA 371
           G K+  +  + +  A
Sbjct: 266 GFKITQNNAMKISFA 280

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 47.4 bits (113), Expect = 4e-07
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V G+P+   E  +++       +    L+KD   G + G G   +  P  T  A    
Sbjct: 19  VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KR 75

Query: 357 NGLKMGDKTLTVRRAT 372
           N + M  + + V  AT
Sbjct: 76  NRMLMIQRYVEVSPAT 91

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 18/102 (17%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKK---FAFVEMRT 231
           V V G+P  A E  +  FF              G  V  V++  +H  +      V+  +
Sbjct: 19  VSVHGMPFSAMENDVRDFFH-------------GLRVDAVHLLKDHVGRNNGNGLVKFLS 65

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPS 273
            ++   A+  + ++     V V   T+     A       PS
Sbjct: 66  PQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGHITSGPS 107

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 46.8 bits (112), Expect = 4e-07
 Identities = 13/84 (15%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            +++  L     + ++K+ L      FG +     +    +   +G  F ++++ +    
Sbjct: 10  TIYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATN 66

Query: 352 ACAALNGLKMGDKTLTVRRATASS 375
           A  ++ G    DK + ++ A   S
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTDS 90

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 17/95 (17%), Positives = 39/95 (41%), Gaps = 23/95 (24%)

Query: 175 RRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK---FAFV 227
             +Y+  L     +    +++   FS+          G    ++++ ++   K    AFV
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRF---------GQ---ILDILVSRSLKMRGQAFV 56

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 258
             + V  A+NA+ ++ G  F    +R+   +  +D
Sbjct: 57  IFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 91

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 296 RVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 63

Query: 355 ALNGLKMGDKTLTVRRATASS 375
             +      K L +  +++++
Sbjct: 64  CESQEMNFGKKLILEVSSSNA 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 16/80 (20%)

Query: 176 RVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R+++G LP    +++ +   FS           G    ++ + I     F F++    + 
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSP---------YGH---IMQINIK--NAFGFIQFDNPQS 57

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
             +A+      +  G  + +
Sbjct: 58  VRDAIECESQEMNFGKKLIL 77

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 296 RVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           R+F+G LP    ++  +  +   +G +   ++           +GF  + +P     A  
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIE 75

Query: 355 ALNGLKMGDKTLTVRRATASS 375
             +      K L +  +++++
Sbjct: 76  XESQEMNFGKKLILEVSSSNA 96

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 16/81 (19%)

Query: 175 RRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            R+++G LP    +++ +   FS           G    ++ + I     F F++    +
Sbjct: 23  SRLFIGNLPLKNVSKEDLFRIFSPY---------GH---IMQINIK--NAFGFIQFDNPQ 68

Query: 234 EASNAMA-LDGIIFEGVAVRV 253
              +A+      +  G  + +
Sbjct: 69  SVRDAIEXESQEMNFGKKLIL 89

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+V GL     E  +     +          G    +  V +   K+ A VE   ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKF---------GT---ICYVMMMPFKRQALVEFENIDS 63

Query: 235 ASNAMA---LDGIIFEGVAVRVR 254
           A   +       +   G      
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFN 86

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 8/75 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 354
           V V GL     E  + E LE FGT      +        K      +++   A   +  A
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGT------ICYVMMMPFKRQALVEFENIDSAKECVTFA 71

Query: 355 ALNGLKMGDKTLTVR 369
           A   + +  +     
Sbjct: 72  ADVPVYIAGQQAFFN 86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.8 bits (111), Expect = 6e-07
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 9/86 (10%)

Query: 290 GAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-- 346
           G+  P RV  +  LP   TE ++  L   FG +    ++K       K   F        
Sbjct: 11  GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEA 64

Query: 347 AVTDIACAALNGLKMGDKTLTVRRAT 372
           A T +         +  + + ++ + 
Sbjct: 65  ANTMVNYYTSVTPVLRGQPIYIQFSN 90

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +++  LP    E  + +              G    V N+ +   K  AF+EM T E 
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPF---------GK---VTNLLMLKGKNQAFIEMNTEEA 64

Query: 235 ASNAMA---LDGIIFEGVAVRVR 254
           A+  +        +  G  + ++
Sbjct: 65  ANTMVNYYTSVTPVLRGQPIYIQ 87

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 46.1 bits (110), Expect = 7e-07
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 15/87 (17%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++A R    +YV G         +   FS       GN       ++++ ++  +  AFV
Sbjct: 9   RRAPRKGNTLYVYGED--MTPTLLRGAFSPF-----GN-------IIDLSMDPPRNCAFV 54

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
               +E A  A+  L+G   E V ++V
Sbjct: 55  TYEKMESADQAVAELNGTQVESVQLKV 81

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 22/104 (21%), Positives = 38/104 (36%), Gaps = 16/104 (15%)

Query: 284 ASGAIGGAEGPDR---VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G    P +   ++V G     T T ++     FG       + D      +   F
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGN------IIDLSMDPPRNCAF 53

Query: 341 CVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
             Y+     D A A LNG ++    L V     +  + +   +S
Sbjct: 54  VTYEKMESADQAVAELNGTQVESVQLKV-----NIARKQPMLDS 92

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 47.5 bits (113), Expect = 7e-07
 Identities = 23/94 (24%), Positives = 32/94 (34%), Gaps = 18/94 (19%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--- 223
               +     V++ GLP  A E  I  FFS +               V V+I        
Sbjct: 39  FTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-------------NPVRVHIEIGPDGRV 85

Query: 224 --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
              A VE  T EEA  AM+ D    +   + +  
Sbjct: 86  TGEADVEFATHEEAVAAMSKDRANMQHRYIELFL 119

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 16/117 (13%), Positives = 32/117 (27%), Gaps = 7/117 (5%)

Query: 268 GPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLV 327
                +    +      S     +     V + GLPY  TE  I         +    + 
Sbjct: 20  HMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIE 78

Query: 328 KDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQSKTEQ 382
              D G   G     +      + A AA+  +   M  + + +   + +   +    
Sbjct: 79  IGPD-GRVTGEADVEFATH---EEAVAAMSKDRANMQHRYIELFLNSTTGASNGAYS 131

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 46.4 bits (110), Expect = 8e-07
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 294 PDRV-FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTD 350
           P RV  +  LP   TET++  L   FG +    ++K       K   F        A+T 
Sbjct: 14  PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITM 67

Query: 351 IACAALNGLKMGDKTLTVRRAT 372
           +   +     + ++ + ++ + 
Sbjct: 68  VNYYSAVTPHLRNQPIYIQYSN 89

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 15/83 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +++  LP    E  +                G    V N+ +   K  AF+E+ T E 
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPF---------GK---VTNILMLKGKNQAFLELATEEA 63

Query: 235 ASNAM---ALDGIIFEGVAVRVR 254
           A   +   +          + ++
Sbjct: 64  AITMVNYYSAVTPHLRNQPIYIQ 86

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 46.8 bits (111), Expect = 9e-07
 Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 15/109 (13%)

Query: 149 PFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAG 208
                  G  P       ++ A   +R +++  LP    E  + +              G
Sbjct: 6   HHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPF---------G 56

Query: 209 PGDAVVNVYINHEKKFAFVEMRTVEEASNAM---ALDGIIFEGVAVRVR 254
               V N+ +   K  AF+EM T E A+  +        +  G  + ++
Sbjct: 57  K---VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ 102

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 11/111 (9%)

Query: 267 LGPGQP--SPNLNLAAVGLASGAIGGAEGPDRV-FVGGLPYYFTETQIKELLESFGTLHG 323
           +G        +  L   G   G    A  P RV  +  LP   TE ++  L   FG +  
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN 60

Query: 324 FDLVKDRDTGNSKGYGFCVYQDP--AVTDIACAALNGLKMGDKTLTVRRAT 372
             ++K       K   F        A T +         +  + + ++ + 
Sbjct: 61  LLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSN 105

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.9 bits (113), Expect = 1e-06
 Identities = 21/123 (17%), Positives = 38/123 (30%), Gaps = 17/123 (13%)

Query: 142 EMAQNMLPFGATQLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTA 201
           E+ +        +      +P      +     R VY+ G P  A    I  +       
Sbjct: 77  ELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK--- 133

Query: 202 IGGNSAGPGDAVVNVYI--NHEKKF---AFVEMRTVEEASNAMALDGIIFEGVAVRVRRP 256
                 G    V+N+ +     K F    FV   ++E A   +   G  ++   + +   
Sbjct: 134 ------GQ---VLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK 184

Query: 257 TDY 259
            DY
Sbjct: 185 DDY 187

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 39.8 bits (92), Expect = 6e-04
 Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 2/78 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++ G P   T   IKE LE  G +    + +       KG  F V+            
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVET 169

Query: 356 LNGLKMGDKTLTVRRATA 373
             G K  +  L +     
Sbjct: 170 P-GQKYKETDLLILFKDD 186

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 23/86 (26%), Positives = 32/86 (37%), Gaps = 18/86 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V++ GLP  A E  I  FFS +               + V+I           A VE  T
Sbjct: 18  VHMRGLPYRATENDIYNFFSPL-------------NPMRVHIEIGPDGRVTGEADVEFAT 64

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
            E+A  AMA D    +   V +   +
Sbjct: 65  HEDAVAAMAKDKANMQHRYVELFLNS 90

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 7/95 (7%)

Query: 285 SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQ 344
           SG+   +     V + GLPY  TE  I              +    D G   G     + 
Sbjct: 6   SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFA 63

Query: 345 DPAVTDIACAAL--NGLKMGDKTLTVRRATASSGQ 377
                + A AA+  +   M  + + +   + +   
Sbjct: 64  TH---EDAVAAMAKDKANMQHRYVELFLNSTAGTS 95

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 9/89 (10%)

Query: 290 GAEGPDR--VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
           G+ G     V + G P+  TE  + E L          +V++   GN  GY F  + +  
Sbjct: 4   GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNE- 60

Query: 348 VTDIACAAL--NGLKMGDKTLTVRRATAS 374
             +    AL  N   MG + + V R  + 
Sbjct: 61  --EEVKQALKCNREYMGGRYIEVFREKSG 87

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 18/86 (20%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-----FAFVEMRT 231
           V + G P    E+ +  F +                 V + I          + FV+   
Sbjct: 13  VKLRGAPFNVTEKNVMEFLA-------------PLKPVAIRIVRNAHGNKTGYIFVDFSN 59

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
            EE   A+  +     G  + V R  
Sbjct: 60  EEEVKQALKCNREYMGGRYIEVFREK 85

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 46.0 bits (109), Expect = 1e-06
 Identities = 13/90 (14%), Positives = 28/90 (31%), Gaps = 8/90 (8%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FA 225
           ++       +   GLP     + +  FFS              + +  +     K+   A
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFS------DCRIRNGENGIHFLLNRDGKRRGDA 58

Query: 226 FVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
            +EM + ++   A+    +      V V  
Sbjct: 59  LIEMESEQDVQKALEKHRMYMGQRYVEVYE 88

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 11/98 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           +   GLP+  T   +             +G   + +RD G  +G      +       A 
Sbjct: 14  IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL 72

Query: 354 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
              + + MG + + V            + ++++   Q 
Sbjct: 73  -EKHRMYMGQRYVEVYEIN------NEDVDALMKSLQV 103

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 46.4 bits (110), Expect = 1e-06
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 7/96 (7%)

Query: 164 QVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK 223
           +V    +  +   V + GLP  A  + +  FF Q          G  + ++ V     + 
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQH-----CPITGGKEGILFVTYPDGRP 67

Query: 224 --FAFVEMRTVEEASNAMALDGIIFEGVAVRVRRPT 257
              AFV     E A NA+     +     + + R T
Sbjct: 68  TGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRST 103

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.9 bits (106), Expect = 4e-06
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 10/84 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFD----LVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           V + GLP+  T  ++         + G       V   D G   G  F ++      + A
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACE---EYA 81

Query: 353 CAAL--NGLKMGDKTLTVRRATAS 374
             AL  +   +G + + + R+TA+
Sbjct: 82  QNALRKHKDLLGKRYIELFRSTAA 105

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 13  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 59

Query: 232 VEEASNAMA-LDGIIFEGVAVRVRR 255
            E+ + A+  LD   F         
Sbjct: 60  KEDMTYAVRKLDNTKFRSHEGETAY 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 7/79 (8%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
             +RV V GLP   +   +K+ +   G +   D+ +D       G G   +        A
Sbjct: 14  SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66

Query: 353 CAALNGLKMGDKTLTVRRA 371
              L+  K           
Sbjct: 67  VRKLDNTKFRSHEGETAYI 85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 8/74 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP--AVTDIACA 354
           V + GL     E  + E L+ FG +    ++        K      ++D   A   +  A
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYA 77

Query: 355 ALNGLKMGDKTLTV 368
           A N + +      V
Sbjct: 78  ADNQIYIAGHPAFV 91

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 44.4 bits (105), Expect = 4e-06
 Identities = 19/82 (23%), Positives = 29/82 (35%), Gaps = 15/82 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V++ GL     E  +     +          GP   +  V +  +K+ A VE   V  
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEF---------GP---ISYVVVMPKKRQALVEFEDVLG 69

Query: 235 ASNAM---ALDGIIFEGVAVRV 253
           A NA+   A + I   G    V
Sbjct: 70  ACNAVNYAADNQIYIAGHPAFV 91

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKEL-LESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +FVG L     +  + E  ++ + +  G  +V D+ TG SKGYGF  + D      A  
Sbjct: 11  SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69

Query: 355 ALNG-LKMGDKTLTVRRAT 372
              G + +G K + +  A 
Sbjct: 70  ECQGAVGLGSKPVRLSVAI 88

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 44.1 bits (104), Expect = 9e-06
 Identities = 16/101 (15%), Positives = 34/101 (33%), Gaps = 9/101 (8%)

Query: 296 RVFVGGLPYYFTETQIKELL----ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
            V +  +     + +++ LL     S G +   D+V D  + ++ G  + V+        
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDL-SDDNSGKAYIVFATQESAQA 87

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
              A  G       L +  +      S+  ++  L     H
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQ--SQVAEDGSLEHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 41.4 bits (97), Expect = 8e-05
 Identities = 16/108 (14%), Positives = 34/108 (31%), Gaps = 23/108 (21%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVY 217
           P    T   T  ++ V +  + P   +      +    S           G    ++++ 
Sbjct: 17  PDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQ---------GD---ILDIV 64

Query: 218 INHEKK---FAFVEMRTVEEASNAM-ALDGIIFEGVAVRV---RRPTD 258
           ++        A++   T E A   + A  G  F+G  + +     P  
Sbjct: 65  VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 6/67 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V  GGL    +  Q+  +LE  G +    +  +      K Y F  Y+    +  A   L
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83

Query: 357 NGLKMGD 363
           NG ++ D
Sbjct: 84  NGKEVVD 90

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 14/68 (20%), Positives = 22/68 (32%), Gaps = 13/68 (19%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V  GGL    +   +                     V  + +   K ++F   RT EE+ 
Sbjct: 30  VANGGLGNGVSRNQLLPVLE------------KCGLVDALLMPPNKPYSFARYRTTEESK 77

Query: 237 NAM-ALDG 243
            A   L+G
Sbjct: 78  RAYVTLNG 85

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 16/95 (16%), Positives = 31/95 (32%), Gaps = 14/95 (14%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-- 223
           M          V + GLP   + + +  F S              D    V+  + ++  
Sbjct: 36  MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDC---------TIHDGAAGVHFIYTREGR 86

Query: 224 ---FAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
               AFVE+ + ++   A+  D        + V +
Sbjct: 87  QSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFK 121

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 11/96 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESF---GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           V + GLP+  +   ++  L          G   +  R+ G   G  F          +A 
Sbjct: 47  VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMAL 105

Query: 354 AALNGLKMGDKTLTVRRATASSGQSKTEQESILAQA 389
              +   MG + + V ++       +TE + +L  +
Sbjct: 106 -KKDRESMGHRYIEVFKS------HRTEMDWVLKHS 134

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 19/85 (22%), Positives = 27/85 (31%), Gaps = 14/85 (16%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R   RV V GLPP  + Q +     +            GD V    + +      VE   
Sbjct: 14  RSENRVVVSGLPPSGSWQDLKDHMREA-----------GD-VCYADV-YRDGTGVVEFVR 60

Query: 232 VEEASNAMA-LDGIIFEGVAVRVRR 255
            E+ + A+  LD   F         
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAY 85

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 20/96 (20%), Positives = 34/96 (35%), Gaps = 16/96 (16%)

Query: 168 QQATRHARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
            Q     R +++  LP    ++ A+                 P   + N  +   K  AF
Sbjct: 19  DQKQELGRVIHLSNLPHSGYSDSAVLKLAE------------PYGKIKNYILMRMKSQAF 66

Query: 227 VEMRTVEEASNAM---ALDGIIFEGVAVRVRRPTDY 259
           +EM T E+A   +       + F+G  V+V     Y
Sbjct: 67  IEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	435
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.98
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.98
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.87
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.85
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.83
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.82
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.82
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.82
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.81
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.81
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.81
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.81
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.81
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.81
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.81
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.81
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.81
2div_A	99	TRNA selenocysteine associated protein; structural	99.81
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.81
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.81
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.8
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.8
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.8
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.8
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.8
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.8
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.79
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.79
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.79
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.79
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.79
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.79
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.79
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.79
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.79
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.79
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.79
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.79
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.79
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.79
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.79
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.78
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.78
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.78
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.78
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.78
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.78
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.78
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.78
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.78
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.78
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.77
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.77
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.77
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.77
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.77
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.76
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.76
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.76
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.76
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.76
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.76
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.76
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.76
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.76
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.75
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.75
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.75
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.75
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.75
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.75
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.74
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.74
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.74
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.73
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.73
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.73
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.73
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.73
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.73
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.73
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.73
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.73
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.72
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.72
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.72
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.72
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.72
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.72
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.72
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.72
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.72
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.72
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.71
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.71
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.71
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.71
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.71
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.7
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.54
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.7
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.7
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.7
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.7
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.69
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.69
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.69
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.69
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.69
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.68
1x5p_A	97	Negative elongation factor E; structure genomics,	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.68
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.68
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.68
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.67
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.65
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.65
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.65
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.65
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.63
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.62
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.62
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.62
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.62
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.62
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.62
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.61
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.61
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.61
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.61
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.6
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.6
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.6
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.6
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.6
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.6
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.59
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.59
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.59
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.59
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.59
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.58
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.58
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.58
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.58
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.58
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.58
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.58
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.57
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.57
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.57
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.57
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.57
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.57
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.57
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.57
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.57
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.57
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.57
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.57
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.57
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.57
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.56
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.56
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.56
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.56
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.56
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.56
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.56
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.56
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.56
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.56
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.56
2div_A	99	TRNA selenocysteine associated protein; structural	99.56
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.56
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.56
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.55
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.55
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.55
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.55
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.55
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.55
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.55
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.55
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.55
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.55
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.55
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.55
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.55
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.54
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.54
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.54
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.54
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.54
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.54
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.54
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.54
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.54
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.54
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.54
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.54
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.54
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.54
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.54
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.54
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.54
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.54
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.54
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.53
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.53
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.53
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.53
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.53
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.52
1x5p_A	97	Negative elongation factor E; structure genomics,	99.52
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.52
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.52
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.52
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.51
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.51
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.51
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.51
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.51
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.51
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.51
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.51
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.51
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.51
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.5
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.5
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.5
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.5
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.5
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.5
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.49
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.49
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.49
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.49
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.49
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.49
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.49
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.49
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.49
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.49
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.48
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.48
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.48
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.48
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.47
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.2
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.47
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.46
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.46
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.46
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.46
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.45
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.44
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.44
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.43
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.43
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.43
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.43
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.43
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.42
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.42
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.4
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.38
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.37
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.37
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.32
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.31
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.3
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.25
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.19
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.18
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.15
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.07
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.06
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.02
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.02
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.98
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.89
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.85
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.75
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.72
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.69
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.62
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.44
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.26
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.01
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.98
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.85
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.73
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.66
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.6
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.25
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.21
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.11
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.02
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.83
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.3
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.01
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	95.61
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.48
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.39
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	94.33
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.96
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	88.35
1jmt_B	28	Splicing factor U2AF 65 kDa subunit; RRM, RNA spli	82.34

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=2.9e-34  Score=253.23  Aligned_cols=194  Identities=46%  Similarity=0.792  Sum_probs=162.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      .+++|||+|||+.+|+++|+++|..||.|.++.. .+...|.++.++.++|||||+|.+.++|.+||.|+|..|.|+.|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~-~~~~~v~~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~   81 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLK   81 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCS-SSSCSEEEEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhccccc-CCCCceEEeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEE
Confidence            4689999999999999999999999999887532 233468999999999999999999999999999999999999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      |.++..+..............+         ...........++|||+|||..+|+++|+++|++||.|..|.|+.++.+
T Consensus        82 v~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~  152 (198)
T 2yh0_A           82 IRRPHDYQPLPGMSENPSVYVP---------GVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT  152 (198)
T ss_dssp             EECCCCCCCCCCSSSCSSCCCT---------TSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTT
T ss_pred             EeCCCCCCCCCCCcCCCcCCCC---------CCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCC
Confidence            9998776432221111000000         0011223356789999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      |.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||.++..
T Consensus       153 ~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          153 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             CSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             CCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999999999999999999999999999999999999987653

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=100.00  E-value=4.8e-34  Score=245.97  Aligned_cols=171  Identities=51%  Similarity=0.910  Sum_probs=153.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ++.++|||+|||+.+|+++|+++|..||.+.++.. .+...|.++.++.++|||||+|.+.++|.+|+.+++..+.|++|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~-~~~~~v~~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i   80 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   80 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhccccc-CCCCceeeeEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCcee
Confidence            35789999999999999999999999998876432 22336889999999999999999999999999999999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~  331 (435)
                      .|.++.....                             .....+|||+|||..+|+++|+++|++||.|..|.|+.++.
T Consensus        81 ~v~~~~~~~~-----------------------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~  131 (172)
T 2g4b_A           81 KIRRPHDYQP-----------------------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA  131 (172)
T ss_dssp             EEECCSSCCC-----------------------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTT
T ss_pred             eecCCcccCC-----------------------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCC
Confidence            9998754421                             12357899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||.
T Consensus       132 ~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            99999999999999999999999999999999999999983

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=5.4e-34  Score=254.17  Aligned_cols=167  Identities=20%  Similarity=0.360  Sum_probs=141.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.++|||+|||+++|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .+++..+.|+.
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~   86 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP   86 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEE------EecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcc
Confidence            3567999999999999999999999999864421      1111224567899999999999999999 69999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR  330 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~  330 (435)
                      |.|.++........                           ....+|||+|||..+|+++|+++|+.||.|+.|.|+.+.
T Consensus        87 i~~~~~~~~~~~~~---------------------------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~  139 (213)
T 4f02_A           87 VRIMWSQRDPSLRK---------------------------SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE  139 (213)
T ss_dssp             CEEEECCCCTHHHH---------------------------HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET
T ss_pred             cccccccccccccc---------------------------cccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC
Confidence            99988754432211                           224589999999999999999999999999999999985


Q ss_pred             CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          331 DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       331 ~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                        +.++|||||+|.+.++|.+||+.|||..|+|+.|.|.+|.+
T Consensus       140 --~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          140 --NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             --TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             --CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence              45799999999999999999999999999999999999954

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=5.5e-33  Score=237.72  Aligned_cols=164  Identities=21%  Similarity=0.366  Sum_probs=142.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      ++|||+|||..+|+++|+++|+.||.|..+.       +.....+.++|||||+|.+.++|..|+ .++|..+.|+.|.|
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~-------i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v   73 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIK-------IMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKI   73 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEE-------EECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEE-------EEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEE
Confidence            5899999999999999999999999753311       111112456799999999999999999 79999999999999


Q ss_pred             cCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC
Q 013837          254 RRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG  333 (435)
Q Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg  333 (435)
                      .++.....                           .......+|||+|||..+|+++|+++|++||.|..+.++.++.+|
T Consensus        74 ~~~~~~~~---------------------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~  126 (166)
T 3md3_A           74 NWAFQSQQ---------------------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG  126 (166)
T ss_dssp             EECCCCCC---------------------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTC
T ss_pred             EEcCCCCC---------------------------CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCC
Confidence            98754321                           122345789999999999999999999999999999999998899


Q ss_pred             CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          334 NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       334 ~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||||+|.+.++|.+|+..|||..|+|+.|.|.||+
T Consensus       127 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          127 SSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             CEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESC
T ss_pred             CcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecC
Confidence            999999999999999999999999999999999999985

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=1.3e-33  Score=248.62  Aligned_cols=177  Identities=21%  Similarity=0.387  Sum_probs=143.5

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+||++++..|.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~   82 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGR   82 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCE
Confidence            345678999999999999999999999999864311      01111134568999999999999999998899999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      .|.|.++........                       .......++|||+|||..+|+++|+++|+.||.|..|.|+.+
T Consensus        83 ~l~v~~~~~~~~~~~-----------------------~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~  139 (196)
T 1l3k_A           83 VVEPKRAVSREDSQR-----------------------PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD  139 (196)
T ss_dssp             ECEEEECCC----------------------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEEC
T ss_pred             EeeeecccCcccccc-----------------------cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeec
Confidence            999998765432110                       112234579999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      ..+|.++|||||+|.+.++|.+||.. +|..|+|+.|.|.+|.++..
T Consensus       140 ~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~~k~~  185 (196)
T 1l3k_A          140 RGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE  185 (196)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC----
T ss_pred             CCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecCChhH
Confidence            88999999999999999999999985 89999999999999977654

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=100.00  E-value=7.9e-33  Score=239.06  Aligned_cols=166  Identities=17%  Similarity=0.355  Sum_probs=147.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||..+|+++|+++|..||.+.+.       .+.+..++.++|||||+|.+.++|.+|++|++..|.|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~-------~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~   81 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGN   81 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTC-------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceE-------EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCe
Confidence            34567899999999999999999999999998762       36778889999999999999999999999999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      +|.|.++.....                           ......++|||+|||..+|+++|+++|+.||.|..+     
T Consensus        82 ~l~v~~~~~~~~---------------------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----  129 (175)
T 1fje_B           82 EIKLEKPKGRDS---------------------------KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----  129 (175)
T ss_dssp             EEEEECCCCSSC---------------------------STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----
T ss_pred             EEEEecCCCccc---------------------------cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----
Confidence            999998765421                           112345799999999999999999999999988655     


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ..+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||.++
T Consensus       130 ~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          130 SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECSSC
T ss_pred             cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecCCC
Confidence            457899999999999999999999999999999999999999765

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=8.2e-33  Score=237.22  Aligned_cols=164  Identities=20%  Similarity=0.323  Sum_probs=142.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      +.++|||+|||..+|+++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|..|+ .+++..+.|++|
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l   75 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRI------MRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL   75 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEE
Confidence            4689999999999999999999999998543211      111123446799999999999999999 599999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD  331 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~  331 (435)
                      .|.++.....                             .....+|||+|||..+|+++|+++|++||.|..+.|+.++.
T Consensus        76 ~v~~~~~~~~-----------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~  126 (168)
T 1b7f_A           76 KVSYARPGGE-----------------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL  126 (168)
T ss_dssp             EEEECCCCSS-----------------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT
T ss_pred             EEEecCCCcc-----------------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCC
Confidence            9998764321                             23457899999999999999999999999999999999988


Q ss_pred             CCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q 013837          332 TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (435)
Q Consensus       332 tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a  371 (435)
                      +|.++|||||+|.+.++|.+|+..|||..|.|  +.|+|.||
T Consensus       127 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          127 TGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             TCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            89999999999999999999999999999988  99999986

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=2.1e-33  Score=251.15  Aligned_cols=184  Identities=26%  Similarity=0.401  Sum_probs=150.3

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCcee
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIF  246 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~  246 (435)
                      .......++|||+|||..+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|++ |++..|
T Consensus        22 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~   95 (216)
T 2qfj_A           22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSID------MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVML   95 (216)
T ss_dssp             HHHHHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEE------ECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCC
T ss_pred             CcccCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEE------EeecCCCCccCceEEEEeCCHHHHHHHHHHccCCee
Confidence            44556789999999999999999999999999854321      01111245678999999999999999995 999999


Q ss_pred             cCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 013837          247 EGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (435)
Q Consensus       247 ~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i  326 (435)
                      .|+.|.|.++...........                  .........++|||+|||..+|+++|+++|++||.|..|.|
T Consensus        96 ~g~~l~v~~~~~~~~~~~~~~------------------~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i  157 (216)
T 2qfj_A           96 GGRNIKVGRPSNIGQAQPIID------------------QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATL  157 (216)
T ss_dssp             C-CCCEEECCSCCGGGHHHHH------------------HHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEE
T ss_pred             CCeeEEEecCCCccccchhhh------------------hhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEE
Confidence            999999998765432211000                  00001234579999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      +.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+.+..
T Consensus       158 ~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          158 ARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             EecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            9998899999999999999999999999999999999999999998764

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.98  E-value=1.5e-31  Score=228.99  Aligned_cols=160  Identities=22%  Similarity=0.368  Sum_probs=139.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~---~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      .++|||+|||+.+|+++|+++|..||.|..         +..+.   .+.++|||||+|.+.++|..|+ .++|..+.|+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~---------v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~   72 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIES---------CKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK   72 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEE---------EEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEE---------EEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCc
Confidence            579999999999999999999999998533         11111   3445699999999999999999 5999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      +|.|.++.+...                             .....+|||+|||..+|+++|+++|++||.|..+.|+.+
T Consensus        73 ~l~v~~~~~~~~-----------------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~  123 (167)
T 1fxl_A           73 TIKVSYARPSSA-----------------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVD  123 (167)
T ss_dssp             ECEEEECCCCCG-----------------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEC
T ss_pred             eEEEEecCCCcc-----------------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEec
Confidence            999998764321                             123468999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE--EEEEEc
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT--LTVRRA  371 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~--l~V~~a  371 (435)
                      ..+|.++|||||+|.+.++|.+|++.|||..|.|+.  |.|.||
T Consensus       124 ~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          124 QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             TTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            888999999999999999999999999999999964  999886

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.98  E-value=3.6e-33  Score=239.22  Aligned_cols=165  Identities=20%  Similarity=0.442  Sum_probs=141.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      +.++|||+|||+.+|+++|+++|+.||.|..+.+      +.+..++.++|||||+|.+.++|.+|+. ++..+.|+.|.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~   74 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKI------MKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVID   74 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEEC------CCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE------EECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcc
Confidence            5689999999999999999999999998543211      1111235678999999999999999996 46789999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      |.++.....                             .....+|||+|||..+|+++|+++|++||.|..+.|+.++.+
T Consensus        75 v~~~~~~~~-----------------------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~  125 (167)
T 2cjk_A           75 PKRAIPRDE-----------------------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDT  125 (167)
T ss_dssp             CEECCCHHH-----------------------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSS
T ss_pred             cccccchhh-----------------------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCC
Confidence            987643211                             112458999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      |.++|||||+|.+.++|.+|++ ++|..|+|+.|.|.||.++
T Consensus       126 g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          126 GQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             STTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             CccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            9999999999999999999998 8999999999999999765

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.97  E-value=7.6e-31  Score=226.45  Aligned_cols=165  Identities=21%  Similarity=0.327  Sum_probs=136.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--CCCcEEEEEecCHHHHHHHH-HhCCceec--
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--HEKKFAFVEMRTVEEASNAM-ALDGIIFE--  247 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~--~~~g~afv~f~~~~~a~~a~-~l~~~~~~--  247 (435)
                      +.++|||+|||+.+|+++|+++|..||.|..+.      .+.+...+  .++|||||+|.+.++|.+|+ .|++..+.  
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~   75 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEIN------VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPG   75 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTT
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccC
Confidence            468999999999999999999999999864411      01111112  56899999999999999999 59998776  


Q ss_pred             -CceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEE
Q 013837          248 -GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDL  326 (435)
Q Consensus       248 -g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i  326 (435)
                       ++.+.+.++....                            .......+|||+|||..+|+++|+++|++||.|..|.|
T Consensus        76 ~~~~~~~~~~~~~~----------------------------~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~  127 (175)
T 3nmr_A           76 MHHPIQMKPADSEK----------------------------NNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRI  127 (175)
T ss_dssp             CSSCCEEEECGGGC----------------------------CSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CccceEEccccccc----------------------------cccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEE
Confidence             5777777654221                            11123568999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC---CeEEEEEEcc
Q 013837          327 VKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTVRRAT  372 (435)
Q Consensus       327 ~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~V~~a~  372 (435)
                      +.++ +|.++|||||+|.+.++|.+|++.|||..+.   |+.|.|.||.
T Consensus       128 ~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          128 LRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             EECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             EECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9986 5999999999999999999999999998776   4999999984

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.97  E-value=1.4e-30  Score=229.63  Aligned_cols=185  Identities=15%  Similarity=0.124  Sum_probs=138.8

Q ss_pred             cCCeEEEcCCC-CCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          173 HARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       173 ~~~~l~V~nlp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      +.++|||+||| ..+|+++|+++|..||.            |..+.+.. .+|||||+|.+.++|..|+ .|||..|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~------------v~~v~i~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   70 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGN------------VEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQ   70 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSC------------EEEEEECTTSTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCC------------eEEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            46799999999 89999999999999997            55555443 5799999999999999999 5999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCC-ccccc---cccc----cCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCe
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPN-LNLAA---VGLA----SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTL  321 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~-~~~~~---~~~~----~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v  321 (435)
                      +|.|.++.................+. .....   ....    ........+..+|||+|||+.+|+++|+++|++||.|
T Consensus        71 ~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v  150 (205)
T 3tyt_A           71 KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVK  150 (205)
T ss_dssp             ECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCC
T ss_pred             eEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCc
Confidence            99999876433210000000000000 00000   0000    0011123456789999999999999999999999999


Q ss_pred             --eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe----EEEEEEc
Q 013837          322 --HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK----TLTVRRA  371 (435)
Q Consensus       322 --~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~----~l~V~~a  371 (435)
                        ..|.|+.+.  +..+|||||+|.+.++|.+||..|||..|.|.    ++.|+||
T Consensus       151 ~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          151 RPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             ceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence              899988874  55679999999999999999999999999886    5777765

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=5.9e-30  Score=238.40  Aligned_cols=189  Identities=21%  Similarity=0.309  Sum_probs=143.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      .....++|||+|||+.+|+++|+    ++|..||.|..         |.....+.++|||||+|.+.++|.+|+ .|||.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~---------v~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   75 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILD---------ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGF   75 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEE---------EEEcCCCCcceEEEEEECCHHHHHHHHHHhcCC
Confidence            34568999999999999999966    89999998643         333336778999999999999999999 79999


Q ss_pred             eecCceEEEcCCCCCCcchhhcCCCCCC----------------------------------------------------
Q 013837          245 IFEGVAVRVRRPTDYNPTLAAALGPGQP----------------------------------------------------  272 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~~~~~~~~~~~~~----------------------------------------------------  272 (435)
                      .|.|+.|.|.++...........+....                                                    
T Consensus        76 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (282)
T 3pgw_A           76 PFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMH  155 (282)
T ss_pred             eeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccc
Confidence            9999999999886544211000000000                                                    


Q ss_pred             ----------CCC----cccccc----------ccc------cCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee
Q 013837          273 ----------SPN----LNLAAV----------GLA------SGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLH  322 (435)
Q Consensus       273 ----------~~~----~~~~~~----------~~~------~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~  322 (435)
                                .+.    ......          ...      ........+.++|||+|||..+|+++|+++|++||.|.
T Consensus       156 ~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~  235 (282)
T 3pgw_A          156 HMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFK  235 (282)
T ss_pred             cCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeE
Confidence                      000    000000          000      00012233567899999999999999999999999999


Q ss_pred             EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEEcc
Q 013837          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRAT  372 (435)
Q Consensus       323 ~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~V~~a~  372 (435)
                      .|.|+.++     +|||||+|.+.++|.+||..|||..|. |+.|+|.||+
T Consensus       236 ~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          236 EVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            99998753     589999999999999999999999999 9999999985

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.97  E-value=1.2e-29  Score=228.59  Aligned_cols=187  Identities=19%  Similarity=0.206  Sum_probs=143.1

Q ss_pred             cccCCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ....++|||+|||+ .+|+++|+++|..||.            |..+.+... +|||||+|.+.++|.+|+ .|++..|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~------------i~~v~i~~~~~g~afV~F~~~~~A~~Ai~~l~g~~~~   98 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLH   98 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCC------------eEEEEEEECCCCEEEEEECCHHHHHHHHHHhCCCeEC
Confidence            35678999999999 9999999999999997            555655544 699999999999999999 59999999


Q ss_pred             CceEEEcCCCCCCcchhhcCCCCCCCCC------ccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-C
Q 013837          248 GVAVRVRRPTDYNPTLAAALGPGQPSPN------LNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-T  320 (435)
Q Consensus       248 g~~l~v~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~  320 (435)
                      |+.|.|.++...................      .................+.++|||+|||..+|+++|+++|++|| .
T Consensus        99 g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~  178 (229)
T 2adc_A           99 GKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV  178 (229)
T ss_dssp             SSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCC
T ss_pred             CeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCC
Confidence            9999999887543211110000000000      00000000000112234568999999999999999999999999 9


Q ss_pred             eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEEccCC
Q 013837          321 LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  374 (435)
Q Consensus       321 v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~V~~a~~~  374 (435)
                      |..|.|+.+     .+|||||+|.+.++|.+|+..|||..|. |+.|+|.|++++
T Consensus       179 i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          179 VKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             eeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            999998663     3689999999999999999999999999 999999999754

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=8.9e-30  Score=234.09  Aligned_cols=156  Identities=22%  Similarity=0.362  Sum_probs=141.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .++|..|.|+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~------------i~~v~i~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~   86 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGE------------PSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSR   86 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCcEEEEEECCHHHHHHHHHHcCCcEECCc
Confidence            356789999999999999999999999997            555667788999999999999999999 5999999999


Q ss_pred             eEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec
Q 013837          250 AVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       250 ~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      .|.|.++.+                                   ..+|||+|||..+|+++|+++|+.||.|..|.|+.+
T Consensus        87 ~l~v~~a~~-----------------------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~  131 (261)
T 3sde_A           87 PLRIRFATH-----------------------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD  131 (261)
T ss_dssp             ECEEEECCC-----------------------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE
T ss_pred             eeEeeeccc-----------------------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC
Confidence            999998642                                   358999999999999999999999999999999999


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHh-CCceeC---CeEEEEEEccCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMG---DKTLTVRRATAS  374 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l-~g~~~~---g~~l~V~~a~~~  374 (435)
                       .+|.++|||||+|.+.++|.+||..| +|..+.   |++|.|.++...
T Consensus       132 -~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          132 -DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             -TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEEECCCE
T ss_pred             -CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEeecccc
Confidence             58999999999999999999999999 455554   999999998754

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=1.7e-29  Score=235.52  Aligned_cols=158  Identities=28%  Similarity=0.407  Sum_probs=145.1

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||             |..+.++.++|||||+|.+.++|..|+ .++|..|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-------------i~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g   84 (284)
T 3smz_A           18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRE   84 (284)
T ss_dssp             HHHCCCEEEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-------------CEEEEEecCCCEEEEEeCCHHHHHHHHHHcCCCeeCC
Confidence            345779999999999999999999999997             445566889999999999999999999 699999999


Q ss_pred             ceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEee
Q 013837          249 VAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVK  328 (435)
Q Consensus       249 ~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~  328 (435)
                      ++|.|.++.                                   ...+|||+|||..+|+++|+++|+.||.|..+.|+.
T Consensus        85 ~~i~v~~~~-----------------------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~  129 (284)
T 3smz_A           85 RELSVQLQP-----------------------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY  129 (284)
T ss_dssp             EECEEEECC-----------------------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEE
T ss_pred             eEEEEEecC-----------------------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEe
Confidence            999998632                                   235899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          329 DRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       329 ~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      ++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++.++.
T Consensus       130 ~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~  176 (284)
T 3smz_A          130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ  176 (284)
T ss_dssp             CTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGG
T ss_pred             eCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCC
Confidence            98899999999999999999999999999999999999999997654

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.97  E-value=6.6e-30  Score=239.28  Aligned_cols=172  Identities=15%  Similarity=0.334  Sum_probs=140.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~  250 (435)
                      ..++|||+|||..+|+++|.++|..|| .|..+.+      + ....+.++|||||+|.+.++|..|+. |+|..|.|+.
T Consensus       116 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i------~-~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  188 (292)
T 2ghp_A          116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL------P-SLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYT  188 (292)
T ss_dssp             CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEEC------C--------CCEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEE------E-eCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            578999999999999999999999999 7654321      1 11225678999999999999999995 9999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeec
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      |.|.++.+.......                      ........+|||+|||.. +|+++|+++|+.||.|..|.|+.+
T Consensus       189 l~v~~a~~~~~~~~~----------------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~  246 (292)
T 2ghp_A          189 LVTKVSNPLEKSKRT----------------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAG  246 (292)
T ss_dssp             CEEEECCCC-------------------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSC
T ss_pred             EEEEECCCCcccccc----------------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEec
Confidence            999987654321110                      012345679999999999 999999999999999999999998


Q ss_pred             CC-CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          330 RD-TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       330 ~~-tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .. ||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.||.++
T Consensus       247 ~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          247 QKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             CC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCC
T ss_pred             CCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCC
Confidence            76 6999999999999999999999 99999999999999999775

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=3.1e-30  Score=240.53  Aligned_cols=172  Identities=17%  Similarity=0.174  Sum_probs=145.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|+|..+.|+.
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~  166 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCF------LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT  166 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEE------EEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            4567999999999999999999999999854310      0111123456899999999999999999 79999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCC-CHHHHHHHHHhcCCeeEEEEeec
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYF-TETQIKELLESFGTLHGFDLVKD  329 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~-te~~l~~~F~~~G~v~~v~i~~~  329 (435)
                      |.|.++.....                          .......++|||+|||..+ |+++|+++|+.||.|..|.|+.+
T Consensus       167 i~v~~a~~~~~--------------------------~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~  220 (284)
T 3smz_A          167 LYVHWTDAGQL--------------------------TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG  220 (284)
T ss_dssp             CEEEECCGGGC--------------------------CTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEEC
T ss_pred             EEEEECCCCCC--------------------------CcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEEC
Confidence            99998754321                          1112446789999999995 99999999999999999999998


Q ss_pred             CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          330 RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       330 ~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      . +|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.|+.++..
T Consensus       221 ~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          221 Q-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             S-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             C-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            6 799999999999999999999999999999999999999977653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=1.8e-29  Score=222.43  Aligned_cols=183  Identities=19%  Similarity=0.211  Sum_probs=140.1

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCC-CcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE-KKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       174 ~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~-~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .++|||+|||+ .+|+++|+++|..||.|            ..+.+... +|||||+|.+.++|.+|+ .|+|..|.|+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i------------~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~   70 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDV------------QRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP   70 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCC------------SEEECSTTCSSCCEEECTTTHHHHHHHHHHTTCCCSSCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCE------------EEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCeecCeE
Confidence            57999999999 99999999999999974            34444333 699999999999999999 59999999999


Q ss_pred             EEEcCCCCCCcchhhcCCCCCCCCCcccccc-------ccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-Cee
Q 013837          251 VRVRRPTDYNPTLAAALGPGQPSPNLNLAAV-------GLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLH  322 (435)
Q Consensus       251 l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~v~  322 (435)
                      |.|.++................. .......       ...........+.++|||+|||..+|+++|+++|+.|| .|.
T Consensus        71 l~v~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~  149 (198)
T 1qm9_A           71 IRITLSKHQNVQLPREGQEDQGL-TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK  149 (198)
T ss_dssp             CEEEECCCCSCCCSSSSSSSSSC-EEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCC
T ss_pred             EEEEEecCCCcCCCCcCCccccc-cccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCce
Confidence            99998765432111100000000 0000000       00000111234578999999999999999999999999 999


Q ss_pred             EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC-CeEEEEEEccCC
Q 013837          323 GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG-DKTLTVRRATAS  374 (435)
Q Consensus       323 ~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~-g~~l~V~~a~~~  374 (435)
                      .|.|+.+     .+|||||+|.+.++|.+|+..|||..|+ |+.|+|.|++++
T Consensus       150 ~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          150 GFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             EEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             EEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            9998764     2789999999999999999999999999 999999999754

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=3.9e-29  Score=233.99  Aligned_cols=157  Identities=20%  Similarity=0.280  Sum_probs=132.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHHHhCCce
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAMALDGII  245 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~~l~~~~  245 (435)
                      .....++|||+|||+.+|+++|+++|..||.|.            .+.+    ..++|||||+|.+.++|.+|+++++..
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~------------~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~  104 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPII------------HVDVADSLKKNFRFARIEFARYDGALAAITKTHKV  104 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEE------------EEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeE------------EEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcE
Confidence            456789999999999999999999999999753            3333    225899999999999999999999999


Q ss_pred             ecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcC-CeeEE
Q 013837          246 FEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFG-TLHGF  324 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~v~~v  324 (435)
                      |.|+.|.|.++.                                    .++|||+|||..+|+++|.++|+.|| .|..|
T Consensus       105 ~~g~~i~v~~~~------------------------------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v  148 (292)
T 2ghp_A          105 VGQNEIIVSHLT------------------------------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSI  148 (292)
T ss_dssp             ETTEECEEEECC------------------------------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEE
T ss_pred             eCCcEEEEEECC------------------------------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEE
Confidence            999999998642                                    46899999999999999999999999 99999


Q ss_pred             EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          325 DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       325 ~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      .|+.++. |.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++.+..
T Consensus       149 ~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  198 (292)
T 2ghp_A          149 RLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE  198 (292)
T ss_dssp             ECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-
T ss_pred             EEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCc
Confidence            9999865 8899999999999999999999999999999999999997654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.91  E-value=1.5e-23  Score=177.54  Aligned_cols=142  Identities=18%  Similarity=0.186  Sum_probs=108.0

Q ss_pred             cCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeE
Q 013837          219 NHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (435)
Q Consensus       219 ~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (435)
                      ...+|||||+|.+.++|.+|+ .+++....+..+.+...........   .             ..............+|
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~---~-------------~~~~~~~~~~~~~~~l   73 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE---G-------------SHHHHHHMDVEGMTSL   73 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEEC---C-------------CCCSSCCCCCCBCCEE
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccc---c-------------ccccccccCCCCCCEE
Confidence            357899999999999999999 5665333222222221111000000   0             0000011223446799


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       298 ~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      ||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.||.++..
T Consensus        74 ~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           74 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             EEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             EEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            9999999999999999999999999999999988999999999999999999999999999999999999999987643

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.87  E-value=6.2e-22  Score=152.96  Aligned_cols=81  Identities=31%  Similarity=0.532  Sum_probs=78.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999996


Q ss_pred             C
Q 013837          373 A  373 (435)
Q Consensus       373 ~  373 (435)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.87  E-value=2.6e-22  Score=168.17  Aligned_cols=136  Identities=15%  Similarity=0.159  Sum_probs=110.6

Q ss_pred             CCCcEEEEEecCHHHHHHHH-Hh-CCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeE
Q 013837          220 HEKKFAFVEMRTVEEASNAM-AL-DGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRV  297 (435)
Q Consensus       220 ~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  297 (435)
                      .-+|+++|+|.+.++|.+|+ ++ ||..+.| .|.+.++.............             ............++|
T Consensus        11 ~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~l   76 (150)
T 2i2y_A           11 TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHH-------------HHHMHRDSCPLDCKV   76 (150)
T ss_dssp             SSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSC-------------CCCSCSSSSTTSCEE
T ss_pred             cccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccc-------------cccccccCCCCCCEE
Confidence            45799999999999999999 68 9999999 99999775432111000000             000112233556899


Q ss_pred             EEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       298 ~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ||+|||+.+|+++|+++|+.||.|..|.|+.+     ++|||||+|.+.++|.+||..|||..|+|+.|.|.|+.++
T Consensus        77 ~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  148 (150)
T 2i2y_A           77 YVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGE  148 (150)
T ss_dssp             EEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCC
T ss_pred             EEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCC
Confidence            99999999999999999999999999999886     5899999999999999999999999999999999999765

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.85  E-value=1.3e-21  Score=148.74  Aligned_cols=82  Identities=20%  Similarity=0.328  Sum_probs=77.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEEEcc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVRRAT  372 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G-~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~V~~a~  372 (435)
                      ++|||+|||..+|+++|+++|++|| .|..|.|++++.||.++|||||+|.+.++|.+||+.| |+..|.|+.|.|.||.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            6899999999999999999999999 7999999999999999999999999999999999987 5678999999999998


Q ss_pred             CCCC
Q 013837          373 ASSG  376 (435)
Q Consensus       373 ~~~~  376 (435)
                      +++.
T Consensus        82 ~~~~   85 (91)
T 2lxi_A           82 PKPK   85 (91)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7754

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.84  E-value=1.2e-20  Score=148.49  Aligned_cols=83  Identities=11%  Similarity=0.123  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      ..+
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            533

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.83  E-value=8.7e-21  Score=144.76  Aligned_cols=82  Identities=20%  Similarity=0.320  Sum_probs=76.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC--eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc----eeCCeE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGT--LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDKT  365 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~--v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~----~~~g~~  365 (435)
                      ..-.+|||+|||+.+|+++|+++|++||.  |..|.|++|+.||.++|||||+|.+.++|.+||+.|||.    .|+|+.
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            44579999999999999999999999995  678999999999999999999999999999999999986    589999


Q ss_pred             EEEEEccC
Q 013837          366 LTVRRATA  373 (435)
Q Consensus       366 l~V~~a~~  373 (435)
                      |.|.||+.
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999964

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.82  E-value=5.9e-20  Score=138.67  Aligned_cols=82  Identities=30%  Similarity=0.455  Sum_probs=76.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +.++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.||.
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            45689999999999999999999999999999999998899999999999999999999999999999999999999997


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            65

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.82  E-value=8.9e-20  Score=136.38  Aligned_cols=81  Identities=21%  Similarity=0.404  Sum_probs=77.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.||.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            58999999999999999999999999999999999889999999999999999999999999999999999999999765


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.82  E-value=9.6e-21  Score=155.10  Aligned_cols=124  Identities=19%  Similarity=0.280  Sum_probs=81.8

Q ss_pred             cEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcC
Q 013837          223 KFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGG  301 (435)
Q Consensus       223 g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~n  301 (435)
                      -++|++|.+...|..|| .++|....|.. .+.+..                             ........++|||+|
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~-----------------------------~~~~~~~~~~l~V~n   54 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGR-----------------------------PPPDVEGMTSLKVDN   54 (135)
T ss_dssp             -------------------------------CCSCC-----------------------------SCSSGGGCCCEEEEC
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCC-----------------------------CCCCCCCCCEEEEeC
Confidence            46788888999999999 58776655543 111111                             111223457899999


Q ss_pred             CCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          302 LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       302 Lp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      ||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|+|.|++.+..
T Consensus        55 Lp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~  129 (135)
T 2lea_A           55 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  129 (135)
T ss_dssp             CCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCC
T ss_pred             CCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999999999999988999999999999999999999999999999999999999987654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.82  E-value=1.9e-19  Score=143.55  Aligned_cols=88  Identities=30%  Similarity=0.437  Sum_probs=82.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34566799999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q 013837          370 RATASSGQ  377 (435)
Q Consensus       370 ~a~~~~~~  377 (435)
                      |+..+...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99877543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.3e-19  Score=139.15  Aligned_cols=84  Identities=20%  Similarity=0.415  Sum_probs=79.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ...+.++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34556799999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EccC
Q 013837          370 RATA  373 (435)
Q Consensus       370 ~a~~  373 (435)
                      ||+.
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9864

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.1e-19  Score=141.91  Aligned_cols=87  Identities=29%  Similarity=0.427  Sum_probs=81.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      |+.++..
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.81  E-value=1.3e-19  Score=140.35  Aligned_cols=85  Identities=26%  Similarity=0.431  Sum_probs=80.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        86 ~~~~~   90 (99)
T 1whw_A           86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCcc
Confidence            87754

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.81  E-value=1.1e-19  Score=139.82  Aligned_cols=82  Identities=32%  Similarity=0.551  Sum_probs=78.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|+|+.|.|.||.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57999999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      +.
T Consensus        82 ~~   83 (96)
T 2x1f_A           82 SD   83 (96)
T ss_dssp             SS
T ss_pred             CC
Confidence            65

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1e-19  Score=141.73  Aligned_cols=87  Identities=29%  Similarity=0.540  Sum_probs=81.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+.|||..|.|+.|+|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      |+.++..
T Consensus        88 ~a~~~~~   94 (102)
T 1x5s_A           88 QAGKSSD   94 (102)
T ss_dssp             EEECCCC
T ss_pred             ECCCCCC
Confidence            9987654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=8.5e-20  Score=142.23  Aligned_cols=86  Identities=19%  Similarity=0.303  Sum_probs=81.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+.|||..|.|+.|.|.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        89 a~~~~~   94 (102)
T 2cqb_A           89 AKPMRI   94 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987754

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.81  E-value=1.1e-19  Score=136.54  Aligned_cols=81  Identities=19%  Similarity=0.336  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.||
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=139.20  Aligned_cols=85  Identities=33%  Similarity=0.644  Sum_probs=80.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            35679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            87653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=9.2e-20  Score=142.28  Aligned_cols=86  Identities=20%  Similarity=0.374  Sum_probs=81.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            45578999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      |+....
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            987643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-19  Score=138.85  Aligned_cols=82  Identities=23%  Similarity=0.448  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            45567999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             cc
Q 013837          371 AT  372 (435)
Q Consensus       371 a~  372 (435)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.6e-19  Score=141.53  Aligned_cols=88  Identities=28%  Similarity=0.425  Sum_probs=82.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ......++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            33456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .++.++..
T Consensus        90 ~~a~~~~~   97 (105)
T 1x5u_A           90 NKASAHNK   97 (105)
T ss_dssp             EETTTTSC
T ss_pred             EECCCCCc
Confidence            99987653

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.81  E-value=2e-19  Score=143.30  Aligned_cols=86  Identities=24%  Similarity=0.476  Sum_probs=80.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+.|||..|.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus       102 a~~~~~  107 (115)
T 2cpz_A          102 KRSKND  107 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCc
Confidence            987653

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.8e-19  Score=139.55  Aligned_cols=85  Identities=25%  Similarity=0.533  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||+ |||..|.|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            3556899999999999999999999999999999999999899999999999999999999999 999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987754

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.81  E-value=1.6e-19  Score=143.64  Aligned_cols=81  Identities=23%  Similarity=0.494  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ...+|||+|||..+|+++|+++|+.||.|..|.|+.++  +.++|||||+|.+.++|.+||+.|||..|.|+.|.|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999985  4589999999999999999999999999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ++.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.81  E-value=1.5e-19  Score=140.08  Aligned_cols=85  Identities=24%  Similarity=0.393  Sum_probs=80.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee-EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE----
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH-GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT----  365 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~-~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~----  365 (435)
                      ....++|||+|||..+|+++|+++|++||.|. .|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45678999999999999999999999999999 9999999989999999999999999999999999999999999    


Q ss_pred             EEEEEccCCC
Q 013837          366 LTVRRATASS  375 (435)
Q Consensus       366 l~V~~a~~~~  375 (435)
                      |+|.||++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997653

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.2e-19  Score=139.81  Aligned_cols=85  Identities=29%  Similarity=0.513  Sum_probs=80.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v-~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+.++|||+|||..+|+++|+++|+.||.|..| .|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|+|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            346799999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987653

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.81  E-value=2.8e-20  Score=141.34  Aligned_cols=81  Identities=17%  Similarity=0.339  Sum_probs=73.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G--~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .+|||+|||..+|+++|+++|++||  .|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            3799999999999999999999999  99999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            664

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=3.5e-19  Score=138.13  Aligned_cols=84  Identities=21%  Similarity=0.540  Sum_probs=79.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.|
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456789999999999999999999999999999999997 899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +.++.
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98764

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.81  E-value=1.9e-19  Score=153.06  Aligned_cols=141  Identities=21%  Similarity=0.174  Sum_probs=80.6

Q ss_pred             EEecCHHHHHHHH-HhCCceec--CceEEEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCC
Q 013837          227 VEMRTVEEASNAM-ALDGIIFE--GVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLP  303 (435)
Q Consensus       227 v~f~~~~~a~~a~-~l~~~~~~--g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp  303 (435)
                      .+|.+.++|..|+ .+++....  |+.+.+.+.......      ...+..+.   ...............++|||+|||
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~------~~~~~~~s---~~~~~~~~~~~~~~~~~l~V~nLp   81 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIH------SYERVRNE---DDDELEPGPQRSVEGWILFVTSIH   81 (165)
T ss_dssp             ----------------------------------------------------------------CCCCC-CEEEEEESCC
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCcccccccc------CccccccC---CCCCCCCCCCCCCCCCEEEEeCCC
Confidence            7899999999999 57776554  555554432111000      00000000   000000011223446789999999


Q ss_pred             CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCCC
Q 013837          304 YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASSG  376 (435)
Q Consensus       304 ~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~~  376 (435)
                      ..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.||..+..
T Consensus        82 ~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A           82 EEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             CCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            9999999999999999999999999988999999999999999999999999999999999999999987754

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.80  E-value=1.9e-19  Score=141.25  Aligned_cols=87  Identities=29%  Similarity=0.453  Sum_probs=80.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee---CCeEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM---GDKTL  366 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~---~g~~l  366 (435)
                      .....++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            345567999999999999999999999999999999999998999999999999999999999999999988   89999


Q ss_pred             EEEEccCCCC
Q 013837          367 TVRRATASSG  376 (435)
Q Consensus       367 ~V~~a~~~~~  376 (435)
                      .|.|+..+..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999987654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=2.1e-19  Score=138.84  Aligned_cols=85  Identities=24%  Similarity=0.448  Sum_probs=79.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC---CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~---tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      .+.++|||+|||..+|+++|+++|+.||.|..|.|+.++.   |+.++|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            4567999999999999999999999999999999999876   6689999999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .++..+..
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99987653

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=3.3e-19  Score=141.15  Aligned_cols=88  Identities=27%  Similarity=0.406  Sum_probs=82.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC------CceeCC
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGD  363 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~------g~~~~g  363 (435)
                      ...+.++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..||      |..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             eEEEEEEccCCCCC
Q 013837          364 KTLTVRRATASSGQ  377 (435)
Q Consensus       364 ~~l~V~~a~~~~~~  377 (435)
                      +.|.|.|+.++...
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999877543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.5e-19  Score=140.65  Aligned_cols=84  Identities=25%  Similarity=0.344  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|.|.||
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.80  E-value=3.2e-19  Score=138.07  Aligned_cols=82  Identities=24%  Similarity=0.418  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~--------v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      ....++|||+|||..+|+++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            355689999999999999999999999999999        999999989999999999999999999999999999999


Q ss_pred             CeEEEEEEcc
Q 013837          363 DKTLTVRRAT  372 (435)
Q Consensus       363 g~~l~V~~a~  372 (435)
                      |+.|+|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999984

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.80  E-value=2.5e-19  Score=140.80  Aligned_cols=84  Identities=33%  Similarity=0.693  Sum_probs=79.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45567999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      ++++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.80  E-value=4.1e-19  Score=139.66  Aligned_cols=86  Identities=23%  Similarity=0.449  Sum_probs=80.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~-~~tg~~~G~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~V  368 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.+ +.+|.++|||||+|.+.++|.+||..| ||..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            355689999999999999999999999999999999998 778999999999999999999999999 999999999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .|+.++..
T Consensus        92 ~~a~~~~~   99 (107)
T 2cph_A           92 EWADSEVT   99 (107)
T ss_dssp             EECCCCCC
T ss_pred             EeCCCCCC
Confidence            99987654

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.80  E-value=5.2e-19  Score=137.94  Aligned_cols=84  Identities=25%  Similarity=0.504  Sum_probs=78.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.++|||+|||..+|+++|+++|+.|| |..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            45568999999999999999999999997 999999999989999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            987653

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.80  E-value=6e-20  Score=142.31  Aligned_cols=80  Identities=16%  Similarity=0.268  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCC------CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC-eEE
Q 013837          294 PDRVFVGGLPY------YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTL  366 (435)
Q Consensus       294 ~~~l~V~nLp~------~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g-~~l  366 (435)
                      .++|||+|||.      .+++++|+++|++||.|..|.|+.++.||.++|||||+|.+.++|.+||+.|||..|.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            46899999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEEccC
Q 013837          367 TVRRATA  373 (435)
Q Consensus       367 ~V~~a~~  373 (435)
                      .|.+|.+
T Consensus        86 ~V~~a~~   92 (100)
T 3ns6_A           86 FLYTMKD   92 (100)
T ss_dssp             EEEESHH
T ss_pred             EEEECch
Confidence            9999954

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.79  E-value=3.8e-19  Score=141.62  Aligned_cols=83  Identities=30%  Similarity=0.572  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            456799999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ++..
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7664

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.79  E-value=4.6e-19  Score=136.13  Aligned_cols=82  Identities=30%  Similarity=0.544  Sum_probs=77.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++. |.++|||||+|.+.++|.+|+..|||..|.|+.|+|.|
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            34567999999999999999999999999999999999975 99999999999999999999999999999999999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      |+.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5e-19  Score=138.08  Aligned_cols=85  Identities=22%  Similarity=0.390  Sum_probs=79.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.+  +|.++|||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3456789999999999999999999999999999999998  79999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      |+.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9987654

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.79  E-value=4.1e-19  Score=140.33  Aligned_cols=84  Identities=27%  Similarity=0.328  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.|+
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            44578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            8764

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.79  E-value=8.4e-19  Score=137.34  Aligned_cols=84  Identities=24%  Similarity=0.388  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC---eEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD---KTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g---~~l~V  368 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456899999999999999999999999999999999997 79999999999999999999999999999988   99999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .||..+..
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99987653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.7e-19  Score=137.74  Aligned_cols=82  Identities=12%  Similarity=0.166  Sum_probs=73.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC--CceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~V  368 (435)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|++.|+  |..|.|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345679999999999999999999999999999999875      6899999999999999999886  47899999999


Q ss_pred             EEccCCCCCC
Q 013837          369 RRATASSGQS  378 (435)
Q Consensus       369 ~~a~~~~~~~  378 (435)
                      .||+.+....
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998876443

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.79  E-value=2.3e-19  Score=145.56  Aligned_cols=87  Identities=20%  Similarity=0.386  Sum_probs=81.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ....+.++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999989999999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .|+.++.
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9997764

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.4e-18  Score=135.50  Aligned_cols=86  Identities=27%  Similarity=0.397  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|.+||..|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            345678999999999999999999999999999999999854  368999999999999999999999999999999999


Q ss_pred             EccCCCCC
Q 013837          370 RATASSGQ  377 (435)
Q Consensus       370 ~a~~~~~~  377 (435)
                      |+..+...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqi_A           89 WATTPSSQ   96 (103)
T ss_dssp             ECCCTTCC
T ss_pred             ECCCCccc
Confidence            99876543

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.79  E-value=7.8e-19  Score=138.01  Aligned_cols=81  Identities=25%  Similarity=0.393  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.|
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4556799999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             cc
Q 013837          371 AT  372 (435)
Q Consensus       371 a~  372 (435)
                      |+
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.79  E-value=4.6e-19  Score=135.04  Aligned_cols=79  Identities=16%  Similarity=0.160  Sum_probs=71.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCce--eCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~V  368 (435)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|++.      +|||||+|++.++|.+|++.|+|..  |.|+.|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            456789999999999999999999999999999998753      6899999999999999999999875  78999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      +||+.+.
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9997654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=4.2e-19  Score=138.77  Aligned_cols=85  Identities=26%  Similarity=0.394  Sum_probs=79.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHh-cCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCce-eCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK-MGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~-~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~-~~g~~l~V  368 (435)
                      ..+.++|||+|||..+|+++|+++|+. ||.|..|.|+.++ +|.++|||||+|.+.++|.+||..|||.. |.|+.|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            345679999999999999999999999 9999999999998 89999999999999999999999999999 99999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99977653

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.4e-19  Score=140.38  Aligned_cols=87  Identities=21%  Similarity=0.356  Sum_probs=81.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~--------~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~  361 (435)
                      .....++|||+|||..+|+++|+++|+.||.|.        .|.|+.++.+|.++|||||+|.+.++|.+||..|||..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999998        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEEEccCCCC
Q 013837          362 GDKTLTVRRATASSG  376 (435)
Q Consensus       362 ~g~~l~V~~a~~~~~  376 (435)
                      .|+.|+|.++..+..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999987653

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=8.2e-19  Score=134.85  Aligned_cols=81  Identities=20%  Similarity=0.256  Sum_probs=75.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~----~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      ...++|||+|||..+++++|+    ++|++||.|..|.|+.++.+   +|||||+|.+.++|.+||+.|||..|.|+.|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            345789999999999999999    99999999999999998764   89999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.+|.+..
T Consensus        84 V~~a~~~~   91 (96)
T 2dgx_A           84 VSLATGAS   91 (96)
T ss_dssp             EEECCCSS
T ss_pred             EEEcCCCC
Confidence            99997664

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=4.9e-19  Score=138.66  Aligned_cols=87  Identities=24%  Similarity=0.521  Sum_probs=81.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.++.++.++|||||+|.+.++|.+||.. ||..|.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~   90 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPK   90 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEE
Confidence            345678999999999999999999999999999999999988999999999999999999999998 9999999999999


Q ss_pred             EccCCCCC
Q 013837          370 RATASSGQ  377 (435)
Q Consensus       370 ~a~~~~~~  377 (435)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 2dh8_A           91 PCTPRGMQ   98 (105)
T ss_dssp             CSCCSSCC
T ss_pred             EccCCCCC
Confidence            99877543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.79  E-value=1.1e-18  Score=131.69  Aligned_cols=80  Identities=24%  Similarity=0.559  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+ +++..|.|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            3556899999999999999999999999999999999999899999999999999999999997 588999999999998


Q ss_pred             c
Q 013837          371 A  371 (435)
Q Consensus       371 a  371 (435)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.79  E-value=6.7e-19  Score=129.00  Aligned_cols=73  Identities=19%  Similarity=0.324  Sum_probs=69.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....|||+||++.+||++|+++|.+||+|..+.|..      ++|||||+|.+.++|.+|++.|||..+.|++|.|.+|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            356899999999999999999999999999999865      5899999999999999999999999999999999999

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.7e-19  Score=137.99  Aligned_cols=83  Identities=28%  Similarity=0.492  Sum_probs=78.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC-CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t-g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+.++|||+|||..+|+++|+++|+.|| |..|.|+.++.+ |.++|||||+|.+.++|.+|| .|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4567999999999999999999999999 999999999887 999999999999999999999 8999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T 1wi8_A           91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             ccCCCC
Confidence            987754

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=3.9e-19  Score=137.39  Aligned_cols=84  Identities=15%  Similarity=0.322  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            34567899999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            9654

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.79  E-value=5.9e-19  Score=133.47  Aligned_cols=83  Identities=23%  Similarity=0.462  Sum_probs=77.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC-cceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN-SKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~-~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ..++|||+|||..+|+++|+++|++||.|..|.|+.+..++. ++|||||+|.+.++|.+|+..|||..|+|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            357899999999999999999999999999999999987665 8999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.78  E-value=8.5e-19  Score=132.87  Aligned_cols=80  Identities=16%  Similarity=0.373  Sum_probs=76.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+ .|||..|.|+.|+|.++.+
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            368999999999999999999999999999999999889999999999999999999999 8999999999999999976


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.78  E-value=9.6e-20  Score=177.97  Aligned_cols=84  Identities=20%  Similarity=0.426  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||+.||+++|.++|++||.|+.|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|.|.||
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ....
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            7654

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.8e-18  Score=134.88  Aligned_cols=87  Identities=24%  Similarity=0.535  Sum_probs=79.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ......++|||+|||..+|+++|+++|+.||.|..|.|+.++.  .++|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3345678999999999999999999999999999999999854  38999999999999999999999999999999999


Q ss_pred             EEccCCCCC
Q 013837          369 RRATASSGQ  377 (435)
Q Consensus       369 ~~a~~~~~~  377 (435)
                      .++.++...
T Consensus        88 ~~a~~~~~~   96 (103)
T 2cq3_A           88 NNATARVMT   96 (103)
T ss_dssp             EECCSSCCC
T ss_pred             EEcccCCCC
Confidence            999877543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.78  E-value=5.4e-19  Score=148.08  Aligned_cols=81  Identities=25%  Similarity=0.430  Sum_probs=76.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..++|||+|||+.+|+++|+++|+.||  .|..|.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      |.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            954

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.78  E-value=1.3e-18  Score=143.53  Aligned_cols=87  Identities=30%  Similarity=0.512  Sum_probs=81.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|+.|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34567899999999999999999999999999999999999899999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      +|..+..
T Consensus       118 ~a~~~~~  124 (139)
T 1u6f_A          118 LAASGHQ  124 (139)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=139.18  Aligned_cols=85  Identities=32%  Similarity=0.591  Sum_probs=79.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..||+ .|.|+.|+|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            345568999999999999999999999999999999999998999999999999999999999999998 8999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      +|..+.
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            997653

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=2.1e-18  Score=137.24  Aligned_cols=85  Identities=22%  Similarity=0.357  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+||..|||..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34556899999999999999999999999999999999997 59999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      ++....
T Consensus        90 ~a~~~~   95 (114)
T 2do0_A           90 MDERAL   95 (114)
T ss_dssp             ECSCCC
T ss_pred             EcccCC
Confidence            997543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.78  E-value=2.2e-19  Score=137.92  Aligned_cols=83  Identities=16%  Similarity=0.339  Sum_probs=76.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34467999999999999999999999999999899999888999999999999999999999999999999999999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      +..
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            853

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.78  E-value=5.3e-19  Score=141.62  Aligned_cols=84  Identities=27%  Similarity=0.468  Sum_probs=78.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ......++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|
T Consensus        35 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33455689999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEcc
Q 013837          369 RRAT  372 (435)
Q Consensus       369 ~~a~  372 (435)
                      .|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9983

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.78  E-value=1.6e-19  Score=143.69  Aligned_cols=108  Identities=19%  Similarity=0.215  Sum_probs=65.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      ..+|||+|||+.+|+++|+++|..||.|..+        .+....+.++|||||+|.+.++|.+|+ .|++..|.|+.|.
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v--------~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~   76 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSC--------KVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVF   76 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEE--------EEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEE--------EEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            4579999999999999999999999986442        111122346899999999999999999 6999999999999


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHH
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQ  310 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~  310 (435)
                      |.++.........                     ........++|||+|||+.+|++.
T Consensus        77 V~~a~~~~~~~~~---------------------~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           77 VGRFKSRKEREAE---------------------LGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             EEESSCCCC-------------------------------------------------
T ss_pred             EEECCCccccccc---------------------cccccCCCCceEeCCCCCCccccc
Confidence            9987654321110                     001122345799999999999863

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.78  E-value=6e-19  Score=143.05  Aligned_cols=86  Identities=24%  Similarity=0.329  Sum_probs=80.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.||
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            44678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 013837          372 TASSGQ  377 (435)
Q Consensus       372 ~~~~~~  377 (435)
                      .++...
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            876543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.78  E-value=7.3e-19  Score=138.40  Aligned_cols=87  Identities=25%  Similarity=0.430  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||..+ |..|+|+.|.|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345679999999999999999999999999999999999989999999999999999999999975 5999999999999


Q ss_pred             ccCCCCCC
Q 013837          371 ATASSGQS  378 (435)
Q Consensus       371 a~~~~~~~  378 (435)
                      +.++..++
T Consensus       101 a~~~~~~~  108 (109)
T 2rs2_A          101 AFPRRAQP  108 (109)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            98876554

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=2.9e-18  Score=133.68  Aligned_cols=86  Identities=23%  Similarity=0.390  Sum_probs=79.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.  ++..|.|+.|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~   88 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCK   88 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEE
Confidence            34566899999999999999999999999999999999999899999999999999999999998  5789999999999


Q ss_pred             EccCCCCC
Q 013837          370 RATASSGQ  377 (435)
Q Consensus       370 ~a~~~~~~  377 (435)
                      ++.++...
T Consensus        89 ~a~~~~~~   96 (103)
T 2cqg_A           89 LPNSKQSQ   96 (103)
T ss_dssp             CCCTTCCC
T ss_pred             ecCCCCcC
Confidence            99877543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.78  E-value=1.5e-18  Score=132.34  Aligned_cols=83  Identities=31%  Similarity=0.608  Sum_probs=77.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+.+  +|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45679999999999999999999999999999999984  7899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .+...
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            87653

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=6.5e-19  Score=137.72  Aligned_cols=81  Identities=42%  Similarity=0.727  Sum_probs=77.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.+|..
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   87 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999965


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      .
T Consensus        88 ~   88 (104)
T 1p1t_A           88 E   88 (104)
T ss_dssp             T
T ss_pred             c
Confidence            5

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.77  E-value=2.9e-18  Score=144.39  Aligned_cols=85  Identities=24%  Similarity=0.372  Sum_probs=80.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|+.|.|+.++.++.++|||||+|.+.++|.+||..|||..|.|+.|+|.||
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .+...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.2e-18  Score=130.21  Aligned_cols=81  Identities=23%  Similarity=0.365  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||..+|+++|+++|+.| .|..|.|+.+ .+|.++|||||+|.+.++|.+||. |||..|+|+.|.|.+|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            456799999999999999999999999 9999999999 689999999999999999999999 9999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ..++
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7764

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.3e-18  Score=132.73  Aligned_cols=82  Identities=13%  Similarity=0.143  Sum_probs=73.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh--CCceeCCeEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLT  367 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~  367 (435)
                      ...+.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|  ++..|.|+.|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   84 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   84 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEE
Confidence            3456789999999999999999999999999999988764      789999999999999999977  57889999999


Q ss_pred             EEEccCCCCC
Q 013837          368 VRRATASSGQ  377 (435)
Q Consensus       368 V~~a~~~~~~  377 (435)
                      |.||+.+...
T Consensus        85 V~~a~~~~~~   94 (101)
T 2cq1_A           85 IQYSNHKELK   94 (101)
T ss_dssp             EEECSCSSCC
T ss_pred             EEEcCcccCc
Confidence            9999876543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=6.8e-19  Score=136.64  Aligned_cols=78  Identities=22%  Similarity=0.258  Sum_probs=74.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|.++|++||.|..|.|+.++. |.++|||||+|.+.++|.+||. ++|..|+|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEch
Confidence            357899999999999999999999999999999999987 9999999999999999999999 99999999999999973

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.77  E-value=4.4e-19  Score=129.80  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|++ |||..|+|+.|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            58999999999999999999999999999999998899999999999999999999998 9999999999999986

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.77  E-value=5.5e-18  Score=136.84  Aligned_cols=86  Identities=22%  Similarity=0.367  Sum_probs=80.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+++++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34566899999999999999999999999999999999998 89999999999999999999999999999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      +|.....
T Consensus       110 ~a~~~~~  116 (124)
T 2kt5_A          110 LVASQID  116 (124)
T ss_dssp             EECCTTC
T ss_pred             EeCCCCC
Confidence            9977643

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.3e-18  Score=137.61  Aligned_cols=85  Identities=18%  Similarity=0.267  Sum_probs=77.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH---HHHHhcCCeeEEEEeecCCCC---CcceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 013837          291 AEGPDRVFVGGLPYYFTETQIK---ELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~---~~F~~~G~v~~v~i~~~~~tg---~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (435)
                      ....++|||+|||+.+++++|.   ++|++||.|..|.|+.++.++   .++|||||+|.+.++|.+||+.|||..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3456799999999999999999   999999999999999987654   4569999999999999999999999999999


Q ss_pred             EEEEEEccCCC
Q 013837          365 TLTVRRATASS  375 (435)
Q Consensus       365 ~l~V~~a~~~~  375 (435)
                      .|+|.||.++.
T Consensus        92 ~l~V~~a~~k~  102 (111)
T 2cpi_A           92 TLKASLGTTKY  102 (111)
T ss_dssp             EEEEESCCCCS
T ss_pred             EEEEEeccccc
Confidence            99999998775

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=1e-18  Score=134.61  Aligned_cols=79  Identities=14%  Similarity=0.100  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc--eeCCeEEE
Q 013837          291 AEGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLT  367 (435)
Q Consensus       291 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~  367 (435)
                      ..+.++|||+|||+ .+|+++|+++|++||.|..|.|+++      +|||||+|++.++|.+||+.||+.  .|.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            34678999999999 9999999999999999999999875      579999999999999999998864  59999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.||....
T Consensus        86 V~~a~~~~   93 (102)
T 1x4d_A           86 VHLSQKYK   93 (102)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCCC
Confidence            99997553

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-18  Score=138.61  Aligned_cols=79  Identities=18%  Similarity=0.365  Sum_probs=75.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.++..
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            478999999999999999999999999999999999989999999999999999999999 8999999999999999854

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2.6e-18  Score=133.30  Aligned_cols=80  Identities=16%  Similarity=0.132  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc--eeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL--KMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~--~~~g~~l~V  368 (435)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|++.  .|.|+.|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456689999999999999999999999999999988764      789999999999999999988654  599999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .|++.+..
T Consensus        86 ~~a~~~~~   93 (104)
T 1wex_A           86 NYSTSKRI   93 (104)
T ss_dssp             EECSSSSC
T ss_pred             EEccCccc
Confidence            99987653

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.4e-18  Score=135.93  Aligned_cols=81  Identities=12%  Similarity=0.162  Sum_probs=73.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC--CceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~V  368 (435)
                      ..+.++|||+|||+.+|+++|+++|++||.|+.|.|+.+      +|||||+|++.++|.+|++.|+  +..|.|++|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            345689999999999999999999999999999999875      7899999999999999999887  46899999999


Q ss_pred             EEccCCCCC
Q 013837          369 RRATASSGQ  377 (435)
Q Consensus       369 ~~a~~~~~~  377 (435)
                      .||+.+...
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999877643

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.76  E-value=4.7e-19  Score=144.50  Aligned_cols=84  Identities=21%  Similarity=0.288  Sum_probs=78.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc----eeCCe
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHG--FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL----KMGDK  364 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~--v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~----~~~g~  364 (435)
                      ....++|||+|||+.+|+++|+++|++||.|..  |.|+.++.+|.++|||||+|.+. +|.+||..|||.    .|.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            356689999999999999999999999999976  99999999999999999999999 999999999999    99999


Q ss_pred             EEEEEEccCCC
Q 013837          365 TLTVRRATASS  375 (435)
Q Consensus       365 ~l~V~~a~~~~  375 (435)
                      .|.|.|+.++.
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997653

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.9e-18  Score=133.39  Aligned_cols=83  Identities=20%  Similarity=0.416  Sum_probs=75.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|..+   +.++|||||+|.+.++|.+||+.|||..|.|+.|+|.|
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999999664   56899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      ++.+..
T Consensus        96 a~~~~~  101 (109)
T 1x4a_A           96 PRSGRG  101 (109)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            987653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.8e-19  Score=134.26  Aligned_cols=81  Identities=21%  Similarity=0.420  Sum_probs=76.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45679999999999999999999999999999999999889999999999999999999999999999999999998876


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.76  E-value=3.6e-18  Score=141.13  Aligned_cols=83  Identities=20%  Similarity=0.365  Sum_probs=77.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ......++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34456789999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EEc
Q 013837          369 RRA  371 (435)
Q Consensus       369 ~~a  371 (435)
                      .||
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            986

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.4e-18  Score=135.46  Aligned_cols=83  Identities=25%  Similarity=0.580  Sum_probs=76.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|++||.|..|.|+.++  +.++|||||+|.+.++|.+|+..|||..|+|+.|.|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999885  4589999999999999999999999999999999999


Q ss_pred             EccCC
Q 013837          370 RATAS  374 (435)
Q Consensus       370 ~a~~~  374 (435)
                      +|.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            99765

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.76  E-value=3.8e-19  Score=135.11  Aligned_cols=80  Identities=33%  Similarity=0.561  Sum_probs=74.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ++|||+|||..+++++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.+ |.+|+..|||..|+|+.|+|.+|.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            47999999999999999999999999999999999989999999999999999 99999999999999999999999765


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.7e-18  Score=134.39  Aligned_cols=83  Identities=16%  Similarity=0.199  Sum_probs=75.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ......+|||+|||+.+|+++|+++|+.||.| .|.|+.++ +|.++|||||+|.+.++|.+||+ +|+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~   87 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEE
Confidence            34556799999999999999999999999954 99999997 89999999999999999999995 89999999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      ++....
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            987654

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.7e-18  Score=135.35  Aligned_cols=83  Identities=19%  Similarity=0.338  Sum_probs=77.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEe-ecCCCCCcceEEEEEEcCHHHHHHHHHHhC--CceeCCeEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLTV  368 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~-v~~v~i~-~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~V  368 (435)
                      ..++|||+|||..+|+++|+++|+.||. |..|.|+ .++.+|.++|||||+|.+.++|.+|+..||  +..|.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V   86 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   86 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEE
Confidence            4578999999999999999999999998 9999998 788889999999999999999999999996  59999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .||.++.
T Consensus        87 ~~a~~~~   93 (109)
T 2dis_A           87 DWAEPEI   93 (109)
T ss_dssp             EESCSSC
T ss_pred             EEcCCCC
Confidence            9998764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.1e-18  Score=136.65  Aligned_cols=83  Identities=27%  Similarity=0.492  Sum_probs=78.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. +|..|.|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            347899999999999999999999999999999999998999999999999999999999997 9999999999999998


Q ss_pred             CCCC
Q 013837          373 ASSG  376 (435)
Q Consensus       373 ~~~~  376 (435)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7754

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.75  E-value=3.7e-18  Score=133.48  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-
Q 013837          292 EGPDRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-  364 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~------te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-  364 (435)
                      ...++|||+|||..+      |+++|+++|++||.|..|.|+  ..+|.++|||||+|.+.++|.+||..|||..|.|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            346799999999999      789999999999999999988  36899999999999999999999999999999998 


Q ss_pred             EEEEEEccCC
Q 013837          365 TLTVRRATAS  374 (435)
Q Consensus       365 ~l~V~~a~~~  374 (435)
                      .|+|.+|...
T Consensus        91 ~l~V~~a~~~  100 (105)
T 2nlw_A           91 TFRVNLFTDF  100 (105)
T ss_dssp             EEEEECSCCC
T ss_pred             eEEEEEcchH
Confidence            9999999754

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.75  E-value=6.7e-19  Score=136.44  Aligned_cols=82  Identities=27%  Similarity=0.498  Sum_probs=75.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~-~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ....++|||+|||..+|+++|+++|+.|| |..|.|+.++ .+|.++|||||+|.+.++|.+|| .|||..|+|+.|.|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34568999999999999999999999999 9999999998 58999999999999999999999 899999999999999


Q ss_pred             EccCC
Q 013837          370 RATAS  374 (435)
Q Consensus       370 ~a~~~  374 (435)
                      ++.++
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99765

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=9.7e-19  Score=128.68  Aligned_cols=76  Identities=28%  Similarity=0.494  Sum_probs=73.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..++ ..|+|+.|.|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999998899999999999999999999999999 9999999999987

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.75  E-value=4.8e-18  Score=137.25  Aligned_cols=81  Identities=21%  Similarity=0.411  Sum_probs=77.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|| .|||..|.|+.|.|.++..
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            478999999999999999999999999999999999889999999999999999999999 7999999999999999976


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=4.5e-18  Score=136.85  Aligned_cols=81  Identities=12%  Similarity=0.229  Sum_probs=73.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~----~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .+.++|||+|||+.+++++|+    ++|++||.|..|.+..   ++.++|||||+|.+.++|..|+..|||..|.|+.|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            456799999999999999876    6999999999888754   578999999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.||..+.
T Consensus       104 V~~a~~~~  111 (127)
T 2a3j_A          104 ITFSETPQ  111 (127)
T ss_dssp             EEECCCCC
T ss_pred             EEEccCcc
Confidence            99997653

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.9e-18  Score=137.29  Aligned_cols=80  Identities=13%  Similarity=0.222  Sum_probs=75.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCe-eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTL-HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v-~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ....++|||+|||+.+|+++|+++|+.||.| ..|.|+.++ +|.++|||||+|.+.++|.+||.. ||..|.|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4556899999999999999999999999999 899999998 899999999999999999999996 9999999999999


Q ss_pred             Ecc
Q 013837          370 RAT  372 (435)
Q Consensus       370 ~a~  372 (435)
                      ++.
T Consensus        90 ~a~   92 (114)
T 2cpy_A           90 VVT   92 (114)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            994

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.6e-18  Score=133.28  Aligned_cols=83  Identities=16%  Similarity=0.312  Sum_probs=76.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~-v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....+|||+|||+.+|+++|+++|+.||.|.. |.|+.+ .+|.++|||||+|.+.++|.+||.. ||..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            45679999999999999999999999999987 888888 6899999999999999999999996 99999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +..+..
T Consensus        91 ~~~~~~   96 (104)
T 1wg5_A           91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHH
Confidence            976643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.75  E-value=4.2e-18  Score=135.99  Aligned_cols=79  Identities=18%  Similarity=0.315  Sum_probs=74.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~---v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45678999999999999999999999999   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EEcc
Q 013837          369 RRAT  372 (435)
Q Consensus       369 ~~a~  372 (435)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9984

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.3e-18  Score=134.04  Aligned_cols=82  Identities=21%  Similarity=0.484  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee--------CC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--------GD  363 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~--------~g  363 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+||..|||..|        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            456899999999999999999999999999999999998 899999999999999999999999999999        68


Q ss_pred             eEEEEEEccCC
Q 013837          364 KTLTVRRATAS  374 (435)
Q Consensus       364 ~~l~V~~a~~~  374 (435)
                      ++|.|.||.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            88999999754

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.5e-17  Score=130.78  Aligned_cols=77  Identities=22%  Similarity=0.289  Sum_probs=72.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC-----eEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTL  366 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l  366 (435)
                      ...++|||+|||+.+|+++|+++|++||.|+.|.|+.+       |||||+|.+.++|.+||+.|||..|.|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            45679999999999999999999999999999999875       799999999999999999999999999     999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|.+|.++.
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999998765

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=7.7e-18  Score=130.77  Aligned_cols=82  Identities=17%  Similarity=0.288  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      .....++|||+|||..+|+++|+++|++||.|   .|+.+ .++.++|||||+|.+.++|.+||..|||..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            34567899999999999999999999999987   56666 578999999999999999999999999999999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      |+.++.
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            998764

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.74  E-value=2e-17  Score=128.93  Aligned_cols=79  Identities=19%  Similarity=0.307  Sum_probs=72.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.|++        |||||+|.+.++|.+||+.|||..|.|+.|.|.|
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            45568999999999999999999999999999998863        5999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 013837          371 ATASSGQ  377 (435)
Q Consensus       371 a~~~~~~  377 (435)
                      +.++...
T Consensus        80 a~~~~~~   86 (103)
T 2dgu_A           80 AKPPDQK   86 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCccc
Confidence            9877543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=126.12  Aligned_cols=77  Identities=29%  Similarity=0.510  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|++||.|..|.|+        +|||||+|.+.++|.+|+..|||..|.|+.|+|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456799999999999999999999999999999987        479999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        78 ~~~~~   82 (90)
T 2dnq_A           78 KNKSK   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=129.76  Aligned_cols=82  Identities=27%  Similarity=0.401  Sum_probs=75.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.++|||+|||..+|+++|+++|+.|+   .|.++.++.++.++|||||+|.+.++|.+||..|||..|.|+.|.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45668999999999999999999999873   678888888899999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      |+++.
T Consensus        89 a~~~~   93 (102)
T 2fc8_A           89 AKPKG   93 (102)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98765

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.5e-17  Score=130.12  Aligned_cols=81  Identities=14%  Similarity=0.091  Sum_probs=73.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC----HHH----HHHHHH--HhCCce
Q 013837          295 DRVFVGGL----PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD----PAV----TDIACA--ALNGLK  360 (435)
Q Consensus       295 ~~l~V~nL----p~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~----~~~----A~~Al~--~l~g~~  360 (435)
                      +.|||+||    |+.+++++|+++|+.||.|..+.++.|++||.++|||||+|.+    +++    |.+|+.  .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            58999999    9999999999999999999999999999999999999999996    333    788888  789999


Q ss_pred             eCCeEEEEEEccCCC
Q 013837          361 MGDKTLTVRRATASS  375 (435)
Q Consensus       361 ~~g~~l~V~~a~~~~  375 (435)
                      |+|+.|+|.+-....
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999975543

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.7e-17  Score=124.48  Aligned_cols=76  Identities=21%  Similarity=0.396  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVR  369 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~V~  369 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|+..| +|..|.|+.|+|.
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            345679999999999999999999999999999999874      789999999999999999999 9999999999999


Q ss_pred             Ecc
Q 013837          370 RAT  372 (435)
Q Consensus       370 ~a~  372 (435)
                      ||+
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.73  E-value=1.4e-17  Score=132.57  Aligned_cols=81  Identities=20%  Similarity=0.401  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|+.||.|..|.|+.+   +.++|||||+|.+.++|.+|+..|||..|.|+.|.|.|+
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45679999999999999999999999999999999876   456999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .+..
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            7643

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.73  E-value=8.5e-19  Score=143.23  Aligned_cols=82  Identities=16%  Similarity=0.197  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.+|+++|+++|++|| |+.|.|+.++. |.++|||||+|.+.++|.+|| .+|+..|+|+.|.|.++
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4457899999999999999999999999 67999999976 999999999999999999999 69999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .....
T Consensus       121 ~~~~~  125 (139)
T 2hgn_A          121 STTGA  125 (139)
T ss_dssp             CCSCC
T ss_pred             CCCCC
Confidence            76643

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.73  E-value=5.6e-18  Score=137.95  Aligned_cols=79  Identities=18%  Similarity=0.286  Sum_probs=75.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~---v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ...++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||+ |||..|+|+.|.|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            44678999999999999999999999999   89999999987 9999999999999999999999 9999999999999


Q ss_pred             EEcc
Q 013837          369 RRAT  372 (435)
Q Consensus       369 ~~a~  372 (435)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9984

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.73  E-value=9.4e-18  Score=131.51  Aligned_cols=79  Identities=16%  Similarity=0.158  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcC-CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFG-TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....+|||+|||+.+|+++|+++|++|| .|..+.|..+    .++|||||+|.+.++|.+||+.|||..|.|+.|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456899999999999999999999999 8999888543    4789999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            9654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.73  E-value=5.7e-18  Score=151.32  Aligned_cols=82  Identities=17%  Similarity=0.331  Sum_probs=77.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcC--CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFG--TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G--~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..++|||+|||+.+|+++|+++|+.||  .|+.|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      |+..
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9543

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2e-18  Score=139.45  Aligned_cols=82  Identities=18%  Similarity=0.309  Sum_probs=75.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .....+|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||. |||..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3456799999999999999999999999999886667766789999999999999999999999 999999999999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      |..
T Consensus       101 a~~  103 (124)
T 1wel_A          101 ITK  103 (124)
T ss_dssp             ECH
T ss_pred             CCH
Confidence            943

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.73  E-value=2.2e-18  Score=126.01  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=72.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+. ++|..|.|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999998899999999999999999999999 5999999999999986

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.6e-17  Score=127.92  Aligned_cols=79  Identities=27%  Similarity=0.526  Sum_probs=72.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC--CeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG--DKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~--g~~l~V  368 (435)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.|..+      +|||||+|.+.++|.+|++.|||..|.  |+.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            345689999999999999999999999999999988754      689999999999999999999999999  999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .|+.++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998764

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=1.2e-18  Score=135.43  Aligned_cols=83  Identities=19%  Similarity=0.330  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||..+|+++|+++|+.||.|.. .++.+..+|.++|||||+|.+.++|.+||+ |||..|.|+.|.|.+|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45679999999999999999999999999887 666776788999999999999999999999 9999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87653

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=128.85  Aligned_cols=80  Identities=33%  Similarity=0.527  Sum_probs=73.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ..+.++|||+|||..+|+++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|++.|||..|.|+.|+|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            355679999999999999999999999999999999864      68999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            987653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=3.5e-18  Score=126.90  Aligned_cols=72  Identities=25%  Similarity=0.401  Sum_probs=67.5

Q ss_pred             CeEEEcCCCCCC------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-EEE
Q 013837          295 DRVFVGGLPYYF------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLT  367 (435)
Q Consensus       295 ~~l~V~nLp~~~------te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~  367 (435)
                      ++|||+|||..+      |+++|+++|++||.|..|.|+  +.+|.++|||||+|.+.++|.+|+..|||..|.|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            589999999999      789999999999999999987  35899999999999999999999999999999999 887


Q ss_pred             E
Q 013837          368 V  368 (435)
Q Consensus       368 V  368 (435)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.4e-18  Score=136.24  Aligned_cols=85  Identities=20%  Similarity=0.258  Sum_probs=73.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|+.||.|..+.+..+..+|.++|||||+|.+.++|.+||..|||..|.|+.|.|.||
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45689999999999999999999999999843322222226889999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      ..+..
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87654

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=129.58  Aligned_cols=79  Identities=18%  Similarity=0.372  Sum_probs=73.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.+      +|||||+|.+.++|.+||..|||..|.|+.|+|.|+
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            45679999999999999999999999999999999876      689999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      +.+..
T Consensus        97 ~~~~~  101 (109)
T 1x4g_A           97 KESPD  101 (109)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            87754

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.72  E-value=9.7e-18  Score=129.21  Aligned_cols=81  Identities=15%  Similarity=0.364  Sum_probs=74.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~----~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .+.++|||+|||..+|+++|+    ++|++||.|..|.|+.   +|.++|||||+|.+.++|.+|+..|||..|.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            456799999999999999999    9999999999998874   477889999999999999999999999999999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.|+.++.
T Consensus        83 v~~a~~~~   90 (97)
T 1nu4_A           83 IQYAKTDS   90 (97)
T ss_dssp             EEECSSCC
T ss_pred             EEEccCCC
Confidence            99997764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=4.1e-17  Score=123.77  Aligned_cols=77  Identities=27%  Similarity=0.406  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|++        +||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            35567999999999999999999999999999999874        3999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +.+..
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=129.83  Aligned_cols=76  Identities=25%  Similarity=0.373  Sum_probs=71.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..+|||+|||+.+|+++|+++|+.| .|..|.|+.++. |.++|||||+|.+.++|.+|| .|||..|+|+.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            3589999999999999999999999 899999999975 999999999999999999999 599999999999999883

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.5e-17  Score=123.59  Aligned_cols=78  Identities=19%  Similarity=0.335  Sum_probs=71.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|++        +||||+|.+.++|.+|+..|||..|.|+.|+|.+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            35567999999999999999999999999999999874        3999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        79 a~~~~~   84 (92)
T 2dgt_A           79 STSRLR   84 (92)
T ss_dssp             SSCCCS
T ss_pred             ccCCCC
Confidence            987653

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.72  E-value=2.3e-17  Score=129.38  Aligned_cols=77  Identities=18%  Similarity=0.446  Sum_probs=72.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..|.|+        +|||||+|.+.++|.+|+..|||..|+|+.|.|.|
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4556899999999999999999999999999999987        58999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +..+.
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            97764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.72  E-value=1.3e-17  Score=129.43  Aligned_cols=77  Identities=19%  Similarity=0.389  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|..      ++|||||+|.+.++|.+|+..|||..|.|+.|+|.||
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3457999999999999999999999999999999873      4789999999999999999999999999999999999


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            653

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.72  E-value=3.5e-17  Score=129.10  Aligned_cols=75  Identities=24%  Similarity=0.460  Sum_probs=69.9

Q ss_pred             CCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          293 GPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ..++|||+|||.. +|+++|+++|++||.|..|.|        ++|||||+|.+.++|.+||+.|||..|+|+.|+|.|+
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4579999999999 999999999999999999988        3789999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ....
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.3e-17  Score=126.15  Aligned_cols=79  Identities=28%  Similarity=0.434  Sum_probs=71.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|. +.++.+    .++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            4467999999999999999999999999997 666654    56899999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1.3e-17  Score=129.41  Aligned_cols=76  Identities=20%  Similarity=0.375  Sum_probs=72.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ++|||+|||..+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+|++.|||..|.|+.|.|.+++.+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999886     5899999999999999999999999999999999999876


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.72  E-value=5.4e-17  Score=124.74  Aligned_cols=76  Identities=16%  Similarity=0.363  Sum_probs=70.4

Q ss_pred             CCCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          291 AEGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       291 ~~~~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ....++|||+|||. .+++++|+++|+.||.|..|.|.        +|||||+|.+.++|.+|+..|||..|.|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34568999999998 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             EccCC
Q 013837          370 RATAS  374 (435)
Q Consensus       370 ~a~~~  374 (435)
                      |++.+
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99764

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=4.7e-18  Score=132.72  Aligned_cols=79  Identities=14%  Similarity=0.220  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC--CceeCCeEEE
Q 013837          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN--GLKMGDKTLT  367 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~--g~~~~g~~l~  367 (435)
                      ..+.++|||+|||+. +|+++|+++|++||.|..|.|++      ++|||||+|.+.++|.+|++.||  +..|.|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            456789999999998 99999999999999999999975      37899999999999999999886  4569999999


Q ss_pred             EEEccCCC
Q 013837          368 VRRATASS  375 (435)
Q Consensus       368 V~~a~~~~  375 (435)
                      |.||..+.
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997664

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.71  E-value=2.1e-17  Score=141.54  Aligned_cols=83  Identities=22%  Similarity=0.353  Sum_probs=78.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|+.|.|+.++ +|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456799999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ....
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7653

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.71  E-value=3.6e-18  Score=134.02  Aligned_cols=80  Identities=16%  Similarity=0.270  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCC---eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGT---LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~---v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      .....+|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++|.+||. |||..|+|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            355679999999999999999999999998   89999999987 9999999999999999999999 999999999999


Q ss_pred             EEEcc
Q 013837          368 VRRAT  372 (435)
Q Consensus       368 V~~a~  372 (435)
                      |.++.
T Consensus        86 V~~a~   90 (107)
T 2lmi_A           86 VYEIN   90 (107)
T ss_dssp             CEECC
T ss_pred             EEECC
Confidence            99984

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=2e-17  Score=130.54  Aligned_cols=77  Identities=18%  Similarity=0.141  Sum_probs=71.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|++||.|..|.|+.      ++|||||+|.+.++|.+||..|||..|.|+.|.|.||..
T Consensus        10 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   83 (111)
T 1whx_A           10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCC
Confidence            46899999999999999999999999999998875      478999999999999999999999999999999999977


Q ss_pred             CCC
Q 013837          374 SSG  376 (435)
Q Consensus       374 ~~~  376 (435)
                      ...
T Consensus        84 ~~~   86 (111)
T 1whx_A           84 GVF   86 (111)
T ss_dssp             TTT
T ss_pred             Ccc
Confidence            643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.71  E-value=1.8e-17  Score=127.36  Aligned_cols=79  Identities=15%  Similarity=0.304  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            456799999999999999999999999988665     246889999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus        89 ~~~~   92 (96)
T 1fjc_A           89 GEKG   92 (96)
T ss_dssp             SSSC
T ss_pred             CCCC
Confidence            7764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=3.6e-17  Score=120.88  Aligned_cols=73  Identities=14%  Similarity=0.195  Sum_probs=65.3

Q ss_pred             CCCe-EEEcCCCCCCCHHH----HHHHHHhc-CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          293 GPDR-VFVGGLPYYFTETQ----IKELLESF-GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       293 ~~~~-l~V~nLp~~~te~~----l~~~F~~~-G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      +..+ |||+|||+.+++++    |+++|++| |.|++|       +|   |+|||+|.+.++|.+|++.|||..|.|+.|
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i   76 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRI   76 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceE
Confidence            3455 99999999999988    55899999 499887       34   999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|.||+.+.
T Consensus        77 ~v~~A~~~s   85 (96)
T 2diu_A           77 IVSFTPKNR   85 (96)
T ss_dssp             EEESSCCSC
T ss_pred             EEEecCCCc
Confidence            999998764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=8.7e-17  Score=128.52  Aligned_cols=78  Identities=22%  Similarity=0.297  Sum_probs=70.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceE-EEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~  370 (435)
                      .-.|||+||++.+|+++|+++|++||.|.+|.|+..     .+|| |||+|.+.++|.+|++.|||..|.|  +.|+|+|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            346889999999999999999999999999988765     2677 9999999999999999999999988  9999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      |+++..
T Consensus       103 ak~~~l  108 (130)
T 3zzy_A          103 SKLTSL  108 (130)
T ss_dssp             CSCSSC
T ss_pred             cCCCce
Confidence            987653

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.9e-17  Score=124.73  Aligned_cols=78  Identities=23%  Similarity=0.393  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG-LKMGDKTLTVR  369 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g-~~~~g~~l~V~  369 (435)
                      ...++|||+|||..+|+++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|++.||| ..|.|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45679999999999999999999999999 6555552       378999999999999999999999 99999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      |+.++..
T Consensus        79 ~a~~~~~   85 (93)
T 2cqh_A           79 YSVSKKL   85 (93)
T ss_dssp             ECCCCCC
T ss_pred             EccCccc
Confidence            9987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.54  E-value=9.9e-19  Score=139.50  Aligned_cols=84  Identities=24%  Similarity=0.413  Sum_probs=78.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeE--------EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHG--------FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~--------v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      .+.++|||+|||..+|+++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++|.+||..|||..|.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34578999999999999999999999999998        8999998899999999999999999999999999999999


Q ss_pred             eEEEEEEccCCC
Q 013837          364 KTLTVRRATASS  375 (435)
Q Consensus       364 ~~l~V~~a~~~~  375 (435)
                      +.|.|.+|.++.
T Consensus        85 ~~l~V~~a~~~~   96 (116)
T 2lcw_A           85 NPIKVSFATRRA   96 (116)
Confidence            999999997654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=2e-17  Score=132.22  Aligned_cols=79  Identities=19%  Similarity=0.286  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCe----eEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTL----HGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v----~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      ....+|||+|||+.+|+++|+++|++||.|    ..|.|+.+. +|.++|||||+|.+.++|.+||.. |+..|+|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            345799999999999999999999999975    689999984 899999999999999999999995 99999999999


Q ss_pred             EEEcc
Q 013837          368 VRRAT  372 (435)
Q Consensus       368 V~~a~  372 (435)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            99983

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.70  E-value=8.9e-17  Score=142.62  Aligned_cols=83  Identities=22%  Similarity=0.275  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|++||.|+.|.|++++.+|.++|||||+|.+.++|.+||..|||..+.|+.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      ...
T Consensus        93 ~~~   95 (213)
T 4f02_A           93 QRD   95 (213)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2e-16  Score=122.22  Aligned_cols=78  Identities=18%  Similarity=0.270  Sum_probs=71.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhc--CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESF--GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ....++|||+|||..+|+++|+++|++|  |.|..|.+.        +|||||+|.+.++|.+||..|||..|.|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3456899999999999999999999999  889888764        569999999999999999999999999999999


Q ss_pred             EEccCCCC
Q 013837          369 RRATASSG  376 (435)
Q Consensus       369 ~~a~~~~~  376 (435)
                      .|+.++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.70  E-value=3.5e-17  Score=127.28  Aligned_cols=80  Identities=29%  Similarity=0.564  Sum_probs=75.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|+.||.|..|.|+.++ +|.++|||||+|.+.++|.+|+.  +|..|+|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            34689999999999999999999999999999999998 89999999999999999999999  9999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      .+.
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            654

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.70  E-value=1.1e-16  Score=132.82  Aligned_cols=78  Identities=22%  Similarity=0.273  Sum_probs=71.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a  371 (435)
                      ..+|||+||++.+|+++|+++|++||.|+.|.|+.+.    ++|||||+|.+.++|.+|++.|||..|.|  +.|+|.||
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            3468999999999999999999999999999987542    57999999999999999999999999965  99999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      +++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8775

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.69  E-value=1.4e-16  Score=123.79  Aligned_cols=81  Identities=15%  Similarity=0.085  Sum_probs=72.6

Q ss_pred             CCCCeEEEcCCCC-----CCCHHHHHHHHHhcCCeeEEEEeecCCC-CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 013837          292 EGPDRVFVGGLPY-----YFTETQIKELLESFGTLHGFDLVKDRDT-GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (435)
Q Consensus       292 ~~~~~l~V~nLp~-----~~te~~l~~~F~~~G~v~~v~i~~~~~t-g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (435)
                      .++++|+|.||..     ..++++|+++|++||.|+.|.|+.++.+ +.++|||||+|.+.++|.+|+..|||..|+|+.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4567999999963     2378999999999999999999998654 688999999999999999999999999999999


Q ss_pred             EEEEEcc
Q 013837          366 LTVRRAT  372 (435)
Q Consensus       366 l~V~~a~  372 (435)
                      |.|.|+.
T Consensus        86 i~v~~a~   92 (105)
T 2pe8_A           86 VKACFYN   92 (105)
T ss_dssp             CEEEECC
T ss_pred             EEEEEcC
Confidence            9999994

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=4.7e-17  Score=124.96  Aligned_cols=77  Identities=16%  Similarity=0.363  Sum_probs=70.8

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+.++|||+|||. .+|+++|+++|++||.|..|.|.        +|||||+|.+.++|.+|+..|||..|.|+.|.|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4567999999998 99999999999999999999884        67999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +..+..
T Consensus        80 a~~~~~   85 (96)
T 2kvi_A           80 SSSNAR   85 (96)
T ss_dssp             EECCCC
T ss_pred             cCcCCC
Confidence            977643

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=9.3e-17  Score=123.39  Aligned_cols=80  Identities=18%  Similarity=0.247  Sum_probs=72.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE-EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGF-DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v-~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ...++|||+|||+.+|+++|+++|+.||.|..| .|+.++.+    |.|||+|.+.++|.+||..|||..|.|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~----~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET----AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS----EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC----CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            345789999999999999999999999999999 58887654    3499999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      |.++.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98763

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.2e-17  Score=126.02  Aligned_cols=79  Identities=23%  Similarity=0.329  Sum_probs=70.5

Q ss_pred             CCCCCeEEE--cCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-----CC
Q 013837          291 AEGPDRVFV--GGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-----GD  363 (435)
Q Consensus       291 ~~~~~~l~V--~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~-----~g  363 (435)
                      ..++++|||  +||++.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+|++.|||..|     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            345678999  779999999999999999999999887642      78999999999999999999999998     78


Q ss_pred             eEEEEEEccCCC
Q 013837          364 KTLTVRRATASS  375 (435)
Q Consensus       364 ~~l~V~~a~~~~  375 (435)
                      .+|.|.|+..-+
T Consensus        96 ~~l~v~~a~~~p  107 (114)
T 2cq2_A           96 ITLYLNFVEKVQ  107 (114)
T ss_dssp             EECEEEEESCCC
T ss_pred             cEEEEEecccCc
Confidence            999999997544

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.69  E-value=2.1e-17  Score=136.96  Aligned_cols=82  Identities=21%  Similarity=0.267  Sum_probs=73.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEE--------EEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGF--------DLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v--------~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      ..+.++|||+|||+.+|+++|+++|+.||.|..+        .+.   .+|.++|||||+|.+.++|.+||..|||..|.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~---~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLM---KEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEE---EETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEec---cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            3556899999999999999999999999998763        333   36889999999999999999999999999999


Q ss_pred             CeEEEEEEccCCC
Q 013837          363 DKTLTVRRATASS  375 (435)
Q Consensus       363 g~~l~V~~a~~~~  375 (435)
                      |+.|.|.||....
T Consensus       119 g~~l~V~~a~~~~  131 (143)
T 3egn_A          119 GKPMVVQFARSAR  131 (143)
T ss_dssp             TEECEEEECCCSC
T ss_pred             CcEEEEEECCCCC
Confidence            9999999997654

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.69  E-value=3.2e-17  Score=131.26  Aligned_cols=80  Identities=19%  Similarity=0.375  Sum_probs=72.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLH--GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~--~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      .....+|||+|||+.+|+++|+++|+.| .|+  .|.|+.++. |.++|||||+|.+.++|.+||+ +++..|+|+.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            3456789999999999999999999999 666  899999986 9999999999999999999999 5889999999999


Q ss_pred             EEccC
Q 013837          369 RRATA  373 (435)
Q Consensus       369 ~~a~~  373 (435)
                      .++..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99853

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.68  E-value=2.3e-16  Score=134.16  Aligned_cols=82  Identities=38%  Similarity=0.599  Sum_probs=78.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            47899999999999999999999999999999999988999999999999999999999999999999999999999976


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ..
T Consensus        82 ~~   83 (167)
T 1fxl_A           82 SS   83 (167)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=3.3e-16  Score=120.47  Aligned_cols=78  Identities=22%  Similarity=0.335  Sum_probs=70.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+||  .+|+++|+++|++||.|..|.|.      .++|||||+|.+.++|.+||..|||..|.|+.|+|.|
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~   83 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   83 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            345679999996  89999999999999999999884      3578999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      +.++..
T Consensus        84 a~~~~~   89 (97)
T 1x5p_A           84 ARKQPM   89 (97)
T ss_dssp             CSSCCC
T ss_pred             CCCCCC
Confidence            987654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.4e-16  Score=121.83  Aligned_cols=78  Identities=24%  Similarity=0.420  Sum_probs=70.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|  +.++.+|.   ||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345799999999999999999999999999987  56655665   99999999999999999 9999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ..+.
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            7654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.68  E-value=1.3e-16  Score=116.90  Aligned_cols=73  Identities=18%  Similarity=0.223  Sum_probs=67.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      .+..|||+||++.+||++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .||+..+.|++|
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~------------V~~~~l~~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I   73 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGP------------LVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLANTTI   73 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCC------------EEEEEEcCCCcEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            3567999999999999999999999997            677777889999999999999999999 699999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      .|..+.
T Consensus        74 ~V~~A~   79 (89)
T 2wbr_A           74 FAESPS   79 (89)
T ss_dssp             EEECCC
T ss_pred             EEEECC
Confidence            999874

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.68  E-value=2.5e-16  Score=125.48  Aligned_cols=75  Identities=19%  Similarity=0.207  Sum_probs=67.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceE-EEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEcc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGY-GFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRAT  372 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~-afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a~  372 (435)
                      .|||+||++.+|+++|+++|++||.|+.|.|+..      .|| |||+|.+.++|..|++.|||..|.|  +.|+|.||+
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4689999999999999999999999999998652      276 9999999999999999999999987  699999998


Q ss_pred             CCCC
Q 013837          373 ASSG  376 (435)
Q Consensus       373 ~~~~  376 (435)
                      ++..
T Consensus       101 ~~~l  104 (124)
T 2e5i_A          101 PTRL  104 (124)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7653

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.68  E-value=1.4e-17  Score=128.38  Aligned_cols=80  Identities=18%  Similarity=0.331  Sum_probs=66.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      -...+|||+|||+++|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|||..|.|++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~   90 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAK------LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT   90 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeE------eeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            3467899999999999999999999999864421      1112224567899999999999999999 59999999999


Q ss_pred             EEEcCCC
Q 013837          251 VRVRRPT  257 (435)
Q Consensus       251 l~v~~~~  257 (435)
                      |.|.++.
T Consensus        91 l~V~~Ak   97 (99)
T 4fxv_A           91 IKVSYAR   97 (99)
T ss_dssp             CEEEECC
T ss_pred             EEEEEee
Confidence            9999875

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.68  E-value=1.9e-16  Score=134.87  Aligned_cols=83  Identities=25%  Similarity=0.432  Sum_probs=79.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +.++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            654

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.67  E-value=1.2e-16  Score=120.50  Aligned_cols=76  Identities=17%  Similarity=0.242  Sum_probs=70.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|++| .|..+.|.      .++|||||+|.+.++|.+|++.|||..|.|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45789999999999999999999999 99999884      468999999999999999999999999999999999996


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            553

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.67  E-value=7.5e-17  Score=122.33  Aligned_cols=80  Identities=21%  Similarity=0.199  Sum_probs=67.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h-CCceecCce
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L-DGIIFEGVA  250 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l-~~~~~~g~~  250 (435)
                      +++|||+|||+.+|+++|+++|+.|| .|..+.      ++.+..++.++|||||+|.+.++|.+||+ + ++..+.|++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~------i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~   74 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVR------LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQK   74 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCC------SSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEE------EEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEE
Confidence            46899999999999999999999999 665532      24445567889999999999999999995 5 567899999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++.+.
T Consensus        75 i~V~~a~~~   83 (91)
T 2lxi_A           75 VSMHYSDPK   83 (91)
T ss_dssp             EEEECCCSC
T ss_pred             EEEEEcCCC
Confidence            999998654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=2.2e-16  Score=121.44  Aligned_cols=77  Identities=19%  Similarity=0.239  Sum_probs=68.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hC--CceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LD--GIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~--~~~~~g  248 (435)
                      ...++|||+|||+.+|+++|+++|.+||.            |.++.+..++|||||+|.+.++|..|++ ++  +..|.|
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~------------V~~v~i~~~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G   81 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGK------------VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRG   81 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            46789999999999999999999999997            6667777789999999999999999995 65  478999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|.|.++....
T Consensus        82 r~l~V~~A~~~~   93 (105)
T 1sjq_A           82 QPIYIQFSNHKE   93 (105)
T ss_dssp             EECCBCCCSSSS
T ss_pred             EEEEEEEcCCCC
Confidence            999999987543

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.65  E-value=1.4e-16  Score=126.56  Aligned_cols=74  Identities=22%  Similarity=0.302  Sum_probs=66.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE-----EE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT-----LT  367 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~-----l~  367 (435)
                      ..++|||+|||+.+|+++|+++|++||.|+.|.|+.+       |||||+|.+.++|.+||+.|||..|.|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3578999999999999999999999999999999765       89999999999999999999999999998     66


Q ss_pred             EEEccC
Q 013837          368 VRRATA  373 (435)
Q Consensus       368 V~~a~~  373 (435)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            666644

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.65  E-value=6e-17  Score=128.90  Aligned_cols=102  Identities=19%  Similarity=0.181  Sum_probs=84.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||..+|+++|+++|..||.|..         +.....+.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~---------v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   77 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---------IRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYL   77 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEE---------EEEECSTTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEE---------EEEeeCCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            5689999999999999999999999998533         222223567899999999999999999 499999999999


Q ss_pred             EEcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCC
Q 013837          252 RVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGT  320 (435)
Q Consensus       252 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~  320 (435)
                      .|.++.....                                     ..+++...++++|.++|++||.
T Consensus        78 ~v~~a~~~~~-------------------------------------~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           78 VVLYYNANRA-------------------------------------FQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             EEEECCHHHH-------------------------------------TTTSCHHHHHHHHHHHHHHHCC
T ss_pred             EEEEecCChh-------------------------------------hhhhhHhHhHHHHHHHHHHhCC
Confidence            9998753210                                     0467777889999999999985

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.65  E-value=1.9e-16  Score=122.81  Aligned_cols=74  Identities=34%  Similarity=0.455  Sum_probs=64.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      ++|||+|||..+|+++|+++|..||.|            ..+.+.. ++|||||+|.+.++|.+|+ .|++..|.|+.|.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   68 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPL------------RTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVR   68 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCC------------SEEEEESSSSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEeeCCCCEEEEEECCHHHHHHHHHHHCCCeECCcEEE
Confidence            489999999999999999999999974            3333333 6999999999999999999 5999999999999


Q ss_pred             EcCCCCCC
Q 013837          253 VRRPTDYN  260 (435)
Q Consensus       253 v~~~~~~~  260 (435)
                      |.++....
T Consensus        69 V~~a~~~~   76 (101)
T 2hvz_A           69 VELSTGMP   76 (101)
T ss_dssp             EEESSSCC
T ss_pred             EEEccCCC
Confidence            99987654

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.65  E-value=6.1e-16  Score=135.28  Aligned_cols=84  Identities=27%  Similarity=0.521  Sum_probs=77.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||.. +|..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            34567999999999999999999999999999999999998999999999999999999999985 99999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +....
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            97653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.65  E-value=3e-16  Score=119.47  Aligned_cols=76  Identities=21%  Similarity=0.150  Sum_probs=67.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce--ecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII--FEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~--~~g  248 (435)
                      .++++|||+|||+.+|+++|.++|.+||.            |.++.+..++|||||+|.+.++|.+|+ .|++..  |.|
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~G   86 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGP------------ISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIYIAG   86 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCEEETT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHhcCCCceeCC
Confidence            46789999999999999999999999997            666777778999999999999999999 587764  789


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|.|.+++..
T Consensus        87 r~i~V~~S~~k   97 (100)
T 3r27_A           87 HPAFVNYSTSQ   97 (100)
T ss_dssp             EEEEEEECSCS
T ss_pred             cEEEEEecccc
Confidence            99999998654

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=9.1e-16  Score=118.97  Aligned_cols=82  Identities=21%  Similarity=0.434  Sum_probs=74.0

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..||.|.. .      .+.+..++.++|||||+|.+.++|.+|++||+..|.|+.|
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~------~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l   87 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-L------AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEI   87 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-C------CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-E------EEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEE
Confidence            45789999999999999999999999999876 2      3677788899999999999999999999999999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++....
T Consensus        88 ~V~~a~~~~   96 (101)
T 1fj7_A           88 KLEKPKGRD   96 (101)
T ss_dssp             EEECCSCCC
T ss_pred             EEEEcCCCC
Confidence            999986543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.64  E-value=6.2e-16  Score=116.67  Aligned_cols=75  Identities=17%  Similarity=0.338  Sum_probs=62.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCce--eCCeEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK--MGDKTLTVR  369 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~--~~g~~l~V~  369 (435)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|.+    |+|..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            45679999999999999999999999999999999875     68999999999999983    45554  569999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      +|.++.
T Consensus        80 ~a~~k~   85 (89)
T 3d2w_A           80 NAEPKH   85 (89)
T ss_dssp             ECC---
T ss_pred             EcCCCC
Confidence            997653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=3.7e-16  Score=123.96  Aligned_cols=78  Identities=27%  Similarity=0.427  Sum_probs=68.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC---CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT---GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t---g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ...++|||+|||+.+|+++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++|.+||+.|+  .++|+.|.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4467899999999999999999999999999 888888776   7999999999999999999999984  477777777


Q ss_pred             EEcc
Q 013837          369 RRAT  372 (435)
Q Consensus       369 ~~a~  372 (435)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6553

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.62  E-value=1.3e-15  Score=133.81  Aligned_cols=78  Identities=17%  Similarity=0.188  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          293 GPDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp-~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +.++|||+||| ..+|+++|+++|++||.|.+|.|+.+     .+|||||+|.+.++|.+||+.|||..|.|+.|.|.|+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            35799999999 89999999999999999999999875     3799999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      +.+.
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.62  E-value=1.1e-16  Score=121.92  Aligned_cols=82  Identities=17%  Similarity=0.281  Sum_probs=66.8

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHh--hcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc---
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTA--IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI---  244 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i--~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~---  244 (435)
                      ...-.||||+|||+.+|+++|+++|++||.+  ..+.      .+.+..++.++|||||+|.+.++|.+|+ .||+.   
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~------i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~   79 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIR------LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPP   79 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEE------CCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSC
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEE------EEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCC
Confidence            4456799999999999999999999999963  2211      1233345778999999999999999999 58885   


Q ss_pred             -eecCceEEEcCCCC
Q 013837          245 -IFEGVAVRVRRPTD  258 (435)
Q Consensus       245 -~~~g~~l~v~~~~~  258 (435)
                       .|+|++|.|.++..
T Consensus        80 ~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           80 LKIDGKTIGVDFAKS   94 (95)
T ss_dssp             EEETTEEEEEEECCC
T ss_pred             ceECCEEEEEEEccC
Confidence             58999999998763

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.62  E-value=1.1e-15  Score=115.00  Aligned_cols=71  Identities=24%  Similarity=0.541  Sum_probs=66.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~----G-------~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~  361 (435)
                      ..++|||+|||..+|+++|+++|+.|    |       .|..+.+..+      +|||||+|.+.++|.+|+ .|||..|
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            45799999999999999999999999    8       8999988764      789999999999999999 8999999


Q ss_pred             CCeEEEEEE
Q 013837          362 GDKTLTVRR  370 (435)
Q Consensus       362 ~g~~l~V~~  370 (435)
                      .|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=1.3e-15  Score=119.94  Aligned_cols=82  Identities=28%  Similarity=0.403  Sum_probs=68.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..         +.......++|||||+|.+.++|.+|+ .||+..|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~---------~~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   88 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---------IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG   88 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEE---------EEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEE---------EEEEECCCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3456789999999999999999999999998533         111223346899999999999999999 799999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        89 ~~l~V~~a~~~~  100 (109)
T 1x4a_A           89 YRLRVEFPRSGR  100 (109)
T ss_dssp             EECEEECCCCCC
T ss_pred             eEEEEEEcccCC
Confidence            999999987643

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.62  E-value=2e-15  Score=128.15  Aligned_cols=80  Identities=23%  Similarity=0.410  Sum_probs=74.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ++|||+|||..+|+++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|.+|+..|||..+.|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999986 4789999999999999999999999999999999999999765


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.61  E-value=6.5e-15  Score=136.50  Aligned_cols=82  Identities=15%  Similarity=0.364  Sum_probs=75.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHH----HHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIK----ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~----~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ..+.++|||+|||..+|+++|+    ++|+.||.|..|.|++   +|.++|||||+|.+.++|.+||..|||..|.|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            3557899999999999999966    8999999999998886   57899999999999999999999999999999999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|.|+....
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999997654

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.61  E-value=4.7e-16  Score=123.69  Aligned_cols=85  Identities=16%  Similarity=0.261  Sum_probs=69.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.      ++.+...+.++|||||+|.+.++|.+|+ .||+..|.|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   94 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK------VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   94 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC
Confidence            345678999999999999999999999999864411      1111124556799999999999999999 699999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        95 ~~l~V~~a~~~~  106 (115)
T 2cpz_A           95 KRLKVQLKRSKN  106 (115)
T ss_dssp             EECEEECCCCSC
T ss_pred             EEEEEEEcCCCC
Confidence            999999987654

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.61  E-value=1.7e-15  Score=117.73  Aligned_cols=81  Identities=11%  Similarity=0.205  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeecCCC--CCcceEEEEEEcCHHHHHHHHHHhCCc
Q 013837          292 EGPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDT--GNSKGYGFCVYQDPAVTDIACAALNGL  359 (435)
Q Consensus       292 ~~~~~l~V~nL--p~~~t--------e~~l~~~F~~~G~v~~v~i~~~~~t--g~~~G~afV~f~~~~~A~~Al~~l~g~  359 (435)
                      .++++|+|.||  |..+.        +++|+++|++||.|+.|.|+++..+  +.++|||||+|.+.++|.+|+..|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            45789999999  33332        4799999999999999999988754  367999999999999999999999999


Q ss_pred             eeCCeEEEEEEcc
Q 013837          360 KMGDKTLTVRRAT  372 (435)
Q Consensus       360 ~~~g~~l~V~~a~  372 (435)
                      .|+|+.|.|.|+.
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999999984

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.61  E-value=1.4e-15  Score=135.04  Aligned_cols=82  Identities=27%  Similarity=0.543  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999865


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ..
T Consensus       108 ~~  109 (216)
T 2qfj_A          108 IG  109 (216)
T ss_dssp             CG
T ss_pred             cc
Confidence            53

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.61  E-value=1.3e-15  Score=119.29  Aligned_cols=78  Identities=18%  Similarity=0.184  Sum_probs=66.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G-~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ....++|||+|||+.+|+++|+++|..|| .|..          +.+....++|||||+|.+.++|.+|+ .|||..|.|
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~----------v~i~~~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~G   94 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTF----------SSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRG   94 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSE----------EECSSCSSSCCEEEEESSHHHHHHHHHHTTTEEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEE----------EEEEcCCCCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            34568999999999999999999999999 6432          11212357999999999999999999 699999999


Q ss_pred             ceEEEcCCCC
Q 013837          249 VAVRVRRPTD  258 (435)
Q Consensus       249 ~~l~v~~~~~  258 (435)
                      +.|.|.++..
T Consensus        95 r~i~V~~a~~  104 (111)
T 2jvr_A           95 SVITVERDDN  104 (111)
T ss_dssp             EEEEEEESCC
T ss_pred             eEEEEEECCC
Confidence            9999998754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.1e-15  Score=115.98  Aligned_cols=78  Identities=21%  Similarity=0.273  Sum_probs=68.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.|.           +.+.++.++|||||+|.+.++|.+|+ .|||..|.|+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-----------~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-----------LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTD   84 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-----------SEEEEETTTTEEEEECSSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-----------EEEEcCCCCcEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            34578999999999999999999999999851           23445688999999999999999999 6999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        85 ~l~V~~a~~~   94 (97)
T 2e5j_A           85 TLRVALARQQ   94 (97)
T ss_dssp             CCEEEECCCC
T ss_pred             EEEEEEcCCC
Confidence            9999987654

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=6.3e-15  Score=115.90  Aligned_cols=81  Identities=25%  Similarity=0.413  Sum_probs=72.4

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .......++|||+|||..+|+++|+++|..||.            |..+.+...+|||||+|.+.++|.+|+ .|++..|
T Consensus        19 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~A~~~l~g~~~   86 (109)
T 1x4g_A           19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTI   86 (109)
T ss_dssp             HHSCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            344567889999999999999999999999997            667777777999999999999999999 6999999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|+.|.|.++....
T Consensus        87 ~g~~l~v~~a~~~~  100 (109)
T 1x4g_A           87 EGHVVKCYWGKESP  100 (109)
T ss_dssp             TTEECEEECCCCCC
T ss_pred             CCcEEEEEecCCCC
Confidence            99999999987654

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=99.60  E-value=3.2e-15  Score=112.43  Aligned_cols=84  Identities=46%  Similarity=0.825  Sum_probs=72.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..||.+.+... .+...|..+.+..++|||||+|.+.++|.+|+.||+..|.|+.|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~-~~~~~v~~~~~~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~l   82 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ-APGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL   82 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCS-SSSCSEEEEEECSSSSEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhccccc-CCCCcceEEEecCCCcEEEEEcCCHHHHHHHHhcCCCEECCeEE
Confidence            46789999999999999999999999976544221 22335888999999999999999999999999999999999999


Q ss_pred             EEcCC
Q 013837          252 RVRRP  256 (435)
Q Consensus       252 ~v~~~  256 (435)
                      .|.++
T Consensus        83 ~V~rp   87 (87)
T 2hzc_A           83 KIRRP   87 (87)
T ss_dssp             EEECC
T ss_pred             EEeCC
Confidence            99863

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.4e-15  Score=117.07  Aligned_cols=77  Identities=17%  Similarity=0.171  Sum_probs=67.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h--CCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L--DGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l--~~~~~~g  248 (435)
                      .+.++|||+|||+.+|+++|+++|.+||.            |..+.+...+|||||+|.+.++|..|++ |  ++..|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------v~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            45789999999999999999999999997            5566666779999999999999999994 4  6788999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|.|.++....
T Consensus        81 r~l~V~~a~~~~   92 (101)
T 2cq1_A           81 QPIYIQYSNHKE   92 (101)
T ss_dssp             EECEEEECSCSS
T ss_pred             cEEEEEEcCccc
Confidence            999999987543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.7e-15  Score=117.36  Aligned_cols=76  Identities=22%  Similarity=0.400  Sum_probs=67.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~------------i~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   91 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGF------------ILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGR   91 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            345689999999999999999999999997            445555688999999999999999999 6999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .|.|.++.+
T Consensus        92 ~l~V~~a~~  100 (101)
T 2la4_A           92 NLRTGWGKE  100 (101)
T ss_dssp             ECCCCBCCC
T ss_pred             EEEEEeccC
Confidence            999998764

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=4.7e-16  Score=119.66  Aligned_cols=77  Identities=22%  Similarity=0.235  Sum_probs=68.0

Q ss_pred             ccCCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCC--ceec
Q 013837          172 RHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG--IIFE  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~--~~~~  247 (435)
                      .+.++|||+|||+ .+|+++|+++|.+||.            |.++.+..++|||||+|.+.++|..|+ .|++  ..|.
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~   80 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALVF   80 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEET
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCC------------EEEEEEEcCCCEEEEEECCHHHHHHHHHHHcCCCceEC
Confidence            3678999999999 9999999999999997            677777778999999999999999999 5765  5699


Q ss_pred             CceEEEcCCCCCC
Q 013837          248 GVAVRVRRPTDYN  260 (435)
Q Consensus       248 g~~l~v~~~~~~~  260 (435)
                      |++|.|.++....
T Consensus        81 Gr~l~V~~a~~~~   93 (102)
T 1x4d_A           81 GKPVRVHLSQKYK   93 (102)
T ss_dssp             TEECEEEEECCCT
T ss_pred             CcEEEEEECCCCC
Confidence            9999999987543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=7.1e-16  Score=116.33  Aligned_cols=78  Identities=19%  Similarity=0.424  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++|++|+.  .+..+.|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            34579999999999999999999999999999999865     58999999999999986433  235569999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.60  E-value=2.9e-15  Score=115.02  Aligned_cols=77  Identities=14%  Similarity=0.327  Sum_probs=66.4

Q ss_pred             hhhcccCCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          168 QQATRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      .......++|||+|||. .+++++|+++|..||.            |..+.+  .+|||||+|.+.++|.+|+ .|||..
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~------------v~~v~i--~~g~afV~f~~~~~A~~Ai~~l~g~~   81 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGH------------IMQINI--KNAFGFIQFDNPQSVRDAIEXESQEM   81 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHTTSE
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCC------------EEEEEE--eCCEEEEEECCHHHHHHHHHHcCCCE
Confidence            34456789999999998 9999999999999997            555555  4899999999999999999 599999


Q ss_pred             ecCceEEEcCCCC
Q 013837          246 FEGVAVRVRRPTD  258 (435)
Q Consensus       246 ~~g~~l~v~~~~~  258 (435)
                      +.|+.|.|.++..
T Consensus        82 ~~g~~l~V~~a~~   94 (97)
T 2xnq_A           82 NFGKKLILEVSSS   94 (97)
T ss_dssp             ETTEECEEEECCC
T ss_pred             ECCEEEEEEecCC
Confidence            9999999998754

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.60  E-value=1.2e-15  Score=122.71  Aligned_cols=81  Identities=15%  Similarity=0.212  Sum_probs=67.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .+.++|||+|||+.+++++|+    ++|++||.|+.         |.....+.++|||||+|.+.++|..|+ .|||..|
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~---------v~i~~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l   97 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---------IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPF   97 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEE---------EEECCCCSSCCCEEEEESSHHHHHHHHHHSTTCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEE---------EEeccCCCcCCEEEEEECCHHHHHHHHHHHCCCEe
Confidence            356899999999999999876    69999998643         222234578999999999999999999 6999999


Q ss_pred             cCceEEEcCCCCCCc
Q 013837          247 EGVAVRVRRPTDYNP  261 (435)
Q Consensus       247 ~g~~l~v~~~~~~~~  261 (435)
                      .|++|.|.|+.....
T Consensus        98 ~gr~l~V~~a~~~~~  112 (127)
T 2a3j_A           98 QGNPLVITFSETPQS  112 (127)
T ss_dssp             TTSCCEEEECCCCCH
T ss_pred             CCCEEEEEEccCcch
Confidence            999999999876543

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.60  E-value=1.7e-15  Score=117.39  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=66.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCC--ceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDG--IIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~--~~~~g  248 (435)
                      .+.++|||+|||+.+++++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|++ |++  ..|.|
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~G   80 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEECCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            45689999999999999999999999997            5566666789999999999999999994 654  56999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|.|.++....
T Consensus        81 r~l~V~~a~~~~   92 (104)
T 1wex_A           81 QQAFFNYSTSKR   92 (104)
T ss_dssp             SBCEEEECSSSS
T ss_pred             EEEEEEEccCcc
Confidence            999999987543

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=6.2e-15  Score=114.67  Aligned_cols=79  Identities=27%  Similarity=0.394  Sum_probs=67.8

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHHH-hCCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAMA-LDGI  244 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~~-l~~~  244 (435)
                      .....++|||+|||..+|+++|+++|..||.|.            .+.+    ..++|||||+|.+.++|.+|+. |++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~------------~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK------------SCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGR   78 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEE------------EEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEe------------EEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCC
Confidence            345678999999999999999999999999853            3333    2367999999999999999994 9999


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|.|+.|.|.++....
T Consensus        79 ~~~g~~l~V~~a~~~~   94 (103)
T 2cqi_A           79 KILGKEVKVNWATTPS   94 (103)
T ss_dssp             EETTEEEEEEECCCTT
T ss_pred             CcCCCeEEEEECCCCc
Confidence            9999999999987643

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.59  E-value=3.4e-15  Score=118.15  Aligned_cols=80  Identities=14%  Similarity=0.118  Sum_probs=70.8

Q ss_pred             CCCeEEEcCCCC--C---CCHHHHHHHHHhcCCeeEEEEeecCC----CCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          293 GPDRVFVGGLPY--Y---FTETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       293 ~~~~l~V~nLp~--~---~te~~l~~~F~~~G~v~~v~i~~~~~----tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ++++|+|.||-.  .   -.++||+++|++||.|..|.|+.+..    ++.++|||||+|.+.++|.+|+..|||.+|+|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            567999999942  2   24689999999999999999999864    45678999999999999999999999999999


Q ss_pred             eEEEEEEcc
Q 013837          364 KTLTVRRAT  372 (435)
Q Consensus       364 ~~l~V~~a~  372 (435)
                      +.|.|.|+.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999984

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=4.7e-15  Score=117.84  Aligned_cols=83  Identities=16%  Similarity=0.268  Sum_probs=71.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.      ..+...++.++|||||+|.+.++|..|+ .|++..|.|+.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   96 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP------IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI   96 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSC------CEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceE------EEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            4568999999999999999999999999975432      2445557888999999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        97 l~v~~a~~~~  106 (115)
T 2cpx_A           97 LVIEFGKNKK  106 (115)
T ss_dssp             CEEEECCCCS
T ss_pred             EEEEEccCCC
Confidence            9999987654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.59  E-value=1.9e-15  Score=118.72  Aligned_cols=81  Identities=10%  Similarity=0.011  Sum_probs=67.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      +.++|||+|||+.+|+++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .|||..|.|+.|
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~------i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i   78 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVE------ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNII   78 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEE------EEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            467999999999999999999999999864421      1122223667899999999999999999 599999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        79 ~V~~a~~~   86 (110)
T 3s8s_A           79 HAQLDIKG   86 (110)
T ss_dssp             EEEECSTT
T ss_pred             EEEECCCC
Confidence            99987543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=8.7e-15  Score=115.57  Aligned_cols=82  Identities=17%  Similarity=0.292  Sum_probs=70.8

Q ss_pred             CCCCCCeEEEcCCCCCCC-----------HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCC
Q 013837          290 GAEGPDRVFVGGLPYYFT-----------ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNG  358 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~t-----------e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g  358 (435)
                      .+.+.++|+|.||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            445678999999954432           6899999999999999965 553   3799999999999999999999999


Q ss_pred             ceeCCeEEEEEEccCCC
Q 013837          359 LKMGDKTLTVRRATASS  375 (435)
Q Consensus       359 ~~~~g~~l~V~~a~~~~  375 (435)
                      ..|.|+.|.|.|+.++.
T Consensus        87 ~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             CEECCcEEEEEEeCCCC
Confidence            99999999999997764

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=7e-16  Score=120.55  Aligned_cols=84  Identities=25%  Similarity=0.379  Sum_probs=68.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   85 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            356789999999999999999999999998543211      111123456799999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        86 ~l~v~~a~~~~   96 (105)
T 1x5u_A           86 PIRVNKASAHN   96 (105)
T ss_dssp             BCEEEETTTTS
T ss_pred             EEEEEECCCCC
Confidence            99999886543

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.59  E-value=6.5e-16  Score=115.73  Aligned_cols=79  Identities=23%  Similarity=0.351  Sum_probs=65.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+++++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|||..|.|++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   78 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   78 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEC------CEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEE------EECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            46789999999999999999999999998543110      111123456899999999999999999 69999999999


Q ss_pred             EEEcCC
Q 013837          251 VRVRRP  256 (435)
Q Consensus       251 l~v~~~  256 (435)
                      |.|.++
T Consensus        79 l~v~~a   84 (85)
T 3mdf_A           79 IRVNLA   84 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEEc
Confidence            999876

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=9.9e-16  Score=120.92  Aligned_cols=77  Identities=18%  Similarity=0.217  Sum_probs=66.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC--CceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g  248 (435)
                      .+.++|||+|||+.+|+++|+++|.+||.|            .++.+..++|||||+|.+.++|.+|+ .++  +..|.|
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V------------~~v~i~~~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G   96 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKV------------TNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRG   96 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCC------------CEEEEEGGGTEEEEECSCHHHHHHHHHHHHHHCCCBTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCE------------EEEEEeCCCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            457899999999999999999999999984            44555556999999999999999999 476  468999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|.|.++....
T Consensus        97 r~l~V~~a~~k~  108 (119)
T 2ad9_A           97 QPIYIQFSNHKE  108 (119)
T ss_dssp             BCCEEEECSSSS
T ss_pred             eEEEEEEccCCC
Confidence            999999987543

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.58  E-value=4.1e-15  Score=114.29  Aligned_cols=76  Identities=21%  Similarity=0.349  Sum_probs=68.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec--C
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE--G  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~--g  248 (435)
                      ...++|||+|||..+|+++|+++|..||.            |..+.+...+|||||+|.+.++|.+|+ .||+..|.  |
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~v~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~g   82 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPD   82 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------eeEEEEeCCCCEEEEEECCHHHHHHHHHHHCCCEeCCCC
Confidence            35689999999999999999999999987            666777777999999999999999999 59999999  9


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++...
T Consensus        83 ~~l~V~~a~~~   93 (97)
T 1why_A           83 RRLRVDFAKSG   93 (97)
T ss_dssp             CBCEEEECCCC
T ss_pred             cEEEEEECCCC
Confidence            99999998754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.58  E-value=2.4e-15  Score=133.43  Aligned_cols=78  Identities=21%  Similarity=0.385  Sum_probs=70.4

Q ss_pred             CCCCeEEEcCCCCCC---------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-
Q 013837          292 EGPDRVFVGGLPYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-  361 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~---------te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~-  361 (435)
                      ...++|||+||+..+         ++++|+++|++||.|+.|.|+..      +|||||+|.+.++|+.|+++|+|..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            456799999999998         79999999999999999999864      79999999999999999999999999 


Q ss_pred             -----------CCeEEEEEEccCCC
Q 013837          362 -----------GDKTLTVRRATASS  375 (435)
Q Consensus       362 -----------~g~~l~V~~a~~~~  375 (435)
                                 .|+.|.|.||+..+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC---
T ss_pred             ccccccccccCCCCEEEEEEccCCC
Confidence                       89999999997654

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.58  E-value=6.8e-15  Score=127.81  Aligned_cols=78  Identities=22%  Similarity=0.260  Sum_probs=72.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++|.+||..+ +..|+|+.|.|.++..
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            4689999999999999999999999999999999986 5899999999999999999999855 5699999999999854

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=2.3e-15  Score=112.71  Aligned_cols=74  Identities=22%  Similarity=0.364  Sum_probs=67.1

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h-CCceecC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L-DGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l-~~~~~~g  248 (435)
                      ....++|||+|||..+|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+. | ++..+.|
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~------------i~~~~~~~~kg~afV~f~~~~~A~~a~~~l~~~~~~~g   76 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGE------------IRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNG   76 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHTTTTTCEETT
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCC------------EeEEEEECCCCEEEEEECCHHHHHHHHHHhcCCeeECC
Confidence            346789999999999999999999999987            6667777789999999999999999995 8 9999999


Q ss_pred             ceEEEcCC
Q 013837          249 VAVRVRRP  256 (435)
Q Consensus       249 ~~l~v~~~  256 (435)
                      ++|.|.|+
T Consensus        77 ~~l~v~~a   84 (85)
T 2ytc_A           77 RRLNVKWG   84 (85)
T ss_dssp             EECCEEEC
T ss_pred             CEEEEEec
Confidence            99999876

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.58  E-value=3.3e-15  Score=117.07  Aligned_cols=77  Identities=23%  Similarity=0.311  Sum_probs=66.3

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ......++|||+|||..+|+++|+++|..||.|.            .+.+.  +|||||+|.+.++|.+|+ .|||..|.
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~------------~v~i~--kg~afV~f~~~~~A~~Ai~~l~g~~~~   91 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMK------------EVKIL--NGFAFVEFEEAESAAKAIEEVHGKSFA   91 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCC------------EEEEE--TTEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEE------------EEEEE--CCEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            4456789999999999999999999999999853            33332  899999999999999999 59999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |+.|.|.++...
T Consensus        92 g~~l~V~~a~~~  103 (108)
T 2jvo_A           92 NQPLEVVYSKLP  103 (108)
T ss_dssp             TEECEEESCSCC
T ss_pred             CeEEEEEEecCC
Confidence            999999998654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=5e-15  Score=113.35  Aligned_cols=82  Identities=23%  Similarity=0.320  Sum_probs=66.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS------IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEE------EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEE------EEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            34578999999999999999999999999853310      0111112456799999999999999999 5999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      +|.|.++..
T Consensus        86 ~l~v~~a~~   94 (95)
T 2cqc_A           86 RIRVSGPSS   94 (95)
T ss_dssp             EEEEECCSC
T ss_pred             EEEEEecCC
Confidence            999998753

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=1.1e-15  Score=117.38  Aligned_cols=82  Identities=15%  Similarity=0.304  Sum_probs=68.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcC-CCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGG-NSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~-~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~  250 (435)
                      ..++|||+|||..+|+++|+++|..||.|..+ .      ++.+..++.++|||||+|.+.++|.+|+. ||+..|.|++
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~------i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   77 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPK------IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRP   77 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCE------ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            56899999999999999999999999987542 1      11111345678999999999999999995 9999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        78 l~v~~a~~~~   87 (96)
T 1x5t_A           78 ITVSYAFKKD   87 (96)
T ss_dssp             CEEEESCCCC
T ss_pred             EEEEEecccC
Confidence            9999987554

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.58  E-value=7.6e-16  Score=112.39  Aligned_cols=75  Identities=15%  Similarity=0.280  Sum_probs=64.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      +|||+|||+.+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+++++..|.|+.|.|.+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   74 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML------MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECC------CBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEEC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEE------EecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEe
Confidence            5999999999999999999999998755322      2222356678999999999999999999999999999999987


Q ss_pred             C
Q 013837          256 P  256 (435)
Q Consensus       256 ~  256 (435)
                      +
T Consensus        75 A   75 (75)
T 2mss_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.58  E-value=9.2e-15  Score=112.05  Aligned_cols=76  Identities=17%  Similarity=0.167  Sum_probs=66.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHH----HHHHHHHHhhcCCCCCCCCceEEEEecCC---CcEEEEEecCHHHHHHHH-HhCC
Q 013837          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVYINHE---KKFAFVEMRTVEEASNAM-ALDG  243 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~v~~~~~~~~---~g~afv~f~~~~~a~~a~-~l~~  243 (435)
                      ...++|||+|||+.+++++|+    ++|..||.            |..+.+..+   +|||||+|.+.++|.+|+ .|||
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~------------v~~v~i~~~~~~rg~afV~f~~~~~A~~Ai~~l~g   74 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGK------------VKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHR   74 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSC------------EEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCc------------EEEEEEEeCCCCCeEEEEEECCHHHHHHHHHHhCC
Confidence            356799999999999999999    99999997            455555432   899999999999999999 5999


Q ss_pred             ceecCceEEEcCCCCC
Q 013837          244 IIFEGVAVRVRRPTDY  259 (435)
Q Consensus       244 ~~~~g~~l~v~~~~~~  259 (435)
                      ..|.|+.|.|.++...
T Consensus        75 ~~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           75 YKIGSKKILVSLATGA   90 (96)
T ss_dssp             EEETTEEEEEEECCCS
T ss_pred             CEECCeEEEEEEcCCC
Confidence            9999999999988654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.5e-15  Score=114.56  Aligned_cols=78  Identities=18%  Similarity=0.403  Sum_probs=68.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEecCHHHHHHHHHhCCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAMALDGI  244 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~------~~~~g~afv~f~~~~~a~~a~~l~~~  244 (435)
                      ....++|||+|||..+|+++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+++++.
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i------------~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~   74 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVV------------TEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFH   74 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCE------------EEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCC
Confidence            3467899999999999999999999999974            34433      45689999999999999999999999


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|.|+.|.|.++....
T Consensus        75 ~~~g~~l~V~~a~~~~   90 (99)
T 2dgs_A           75 DIMGKKVEVKRAEPRD   90 (99)
T ss_dssp             BSSSCBCEEEECCCCC
T ss_pred             EECCeEEEEEECCCCc
Confidence            9999999999887553

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.2e-14  Score=112.14  Aligned_cols=77  Identities=25%  Similarity=0.386  Sum_probs=67.1

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHH--HHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCcee
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQV--MTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIF  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~  246 (435)
                      .....++|||+|||+.+|+++|+++|..|  |.            |..+.+  .+|||||+|.+.++|.+|+. ||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~------------v~~~~~--~~g~afV~f~~~~~A~~A~~~l~g~~~   76 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------------VERVKK--IRDYAFVHFSNREDAVEAMKALNGKVL   76 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTC------------EEEEEE--CSSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             ccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcc------------eEEEEE--eCCeEEEEeCCHHHHHHHHHHhCCCEe
Confidence            34567899999999999999999999999  65            555554  47899999999999999994 999999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|+.|.|.++....
T Consensus        77 ~g~~l~v~~a~~~~   90 (99)
T 2cpd_A           77 DGSPIEVTLAKPVD   90 (99)
T ss_dssp             TTEEEEEECCCCCC
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999987643

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.57  E-value=7.9e-15  Score=125.61  Aligned_cols=82  Identities=24%  Similarity=0.478  Sum_probs=75.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC--CcceEEEEEEcCHHHHHHHHHHhCCceeC---CeEEEE
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGLKMG---DKTLTV  368 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg--~~~G~afV~f~~~~~A~~Al~~l~g~~~~---g~~l~V  368 (435)
                      .++|||+|||..+|+++|+++|++||.|..|.|+.++.+|  .++|||||+|.+.++|.+|++.|||..+.   ++.|.|
T Consensus         3 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~   82 (175)
T 3nmr_A            3 AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQM   82 (175)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEE
Confidence            4689999999999999999999999999999999998876  89999999999999999999999998876   688899


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .++....
T Consensus        83 ~~~~~~~   89 (175)
T 3nmr_A           83 KPADSEK   89 (175)
T ss_dssp             EECGGGC
T ss_pred             ccccccc
Confidence            8886554

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.1e-15  Score=118.74  Aligned_cols=83  Identities=22%  Similarity=0.332  Sum_probs=69.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..|.|+.
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   83 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEEC------CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEE------EecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            46789999999999999999999999998644221      112233567899999999999999999 69999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        84 l~V~~a~~~~   93 (102)
T 2cqb_A           84 IRVNLAKPMR   93 (102)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEeCCCCC
Confidence            9999987654

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=2.8e-15  Score=118.17  Aligned_cols=76  Identities=21%  Similarity=0.153  Sum_probs=69.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   74 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHHV   74 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEeCCCCEEEEEeCCHHHHHHHHHHhCCCEECCe
Confidence            445789999999999999999999999997            667777789999999999999999999 6999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .|.|.|+..
T Consensus        75 ~l~V~~a~~   83 (111)
T 1whx_A           75 PLYLEWAPI   83 (111)
T ss_dssp             BCEEEEEET
T ss_pred             EEEEEECCC
Confidence            999998754

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=7.8e-15  Score=114.10  Aligned_cols=79  Identities=24%  Similarity=0.365  Sum_probs=68.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~----~~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      .....++|||+|||..+|+++|+++|..||.|            ..+.+.    .++|||||+|.+.++|.+|+ .|++.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v------------~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~   78 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKI------------LDVEIIFNERGSKGFGFVTFENSADADRAREKLHGT   78 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCE------------EEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            34567899999999999999999999999974            344332    35899999999999999999 59999


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|.|+.|.|.++....
T Consensus        79 ~~~g~~l~v~~a~~~~   94 (103)
T 2cq3_A           79 VVEGRKIEVNNATARV   94 (103)
T ss_dssp             EETTEECEEEECCSSC
T ss_pred             EECCEEEEEEEcccCC
Confidence            9999999999987654

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.57  E-value=1.3e-15  Score=115.30  Aligned_cols=80  Identities=15%  Similarity=0.157  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      .+|||+|||+.+|+++|+++|..||  .|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|||..|.|+.|
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~------i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i   75 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK------FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNP   75 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEE------EEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEE------EEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEE
Confidence            4799999999999999999999999  654311      1111125667899999999999999999 699999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++.+..
T Consensus        76 ~V~~~~~~~   84 (90)
T 3p5t_L           76 VVTPSNKLE   84 (90)
T ss_dssp             EECCC----
T ss_pred             EEEECCCCc
Confidence            999876543

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=2.3e-15  Score=116.25  Aligned_cols=77  Identities=29%  Similarity=0.480  Sum_probs=68.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.            |..+.+..++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~   79 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGK   79 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCC------------eEEEEEecCCCEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            346789999999999999999999999997            455666678999999999999999999 6999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        80 ~l~v~~a~~~   89 (99)
T 2cpj_A           80 QLRVRFACHS   89 (99)
T ss_dssp             CCEEEESSCC
T ss_pred             eEEEEEcCCC
Confidence            9999988654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.57  E-value=2.5e-14  Score=117.70  Aligned_cols=85  Identities=15%  Similarity=0.239  Sum_probs=68.7

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .||+..|.|
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  111 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK------IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE------EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            445678999999999999999999999999854310      0111112445899999999999999999 599999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus       112 ~~l~v~~a~~~~  123 (139)
T 1u6f_A          112 KRLKVALAASGH  123 (139)
T ss_dssp             CEEEEEESSCCC
T ss_pred             eEEEEEECCCCC
Confidence            999999887654

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=1.9e-15  Score=116.43  Aligned_cols=81  Identities=16%  Similarity=0.119  Sum_probs=69.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   86 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV------CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK   86 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTC------EEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceE------EEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            4568999999999999999999999999875421      2344445667899999999999999999 69999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.++..
T Consensus        87 l~V~~a~~   94 (98)
T 2cqp_A           87 VKLVLGSG   94 (98)
T ss_dssp             CEEEESSC
T ss_pred             EEEEEcCC
Confidence            99998754

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.57  E-value=1.8e-15  Score=122.07  Aligned_cols=85  Identities=21%  Similarity=0.350  Sum_probs=69.8

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      ......++|||+|||..+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|++|+|..|.|
T Consensus        31 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g  104 (124)
T 2jwn_A           31 KKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT------ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRG  104 (124)
T ss_dssp             HHHHHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEE------EEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETT
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECC
Confidence            3445678999999999999999999999999864411      0111124567899999999999999999999999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++...
T Consensus       105 ~~l~V~~a~~~  115 (124)
T 2jwn_A          105 RTIKVLPKRTN  115 (124)
T ss_dssp             EECEEEESSCC
T ss_pred             eEEEEEECCCC
Confidence            99999987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=8.1e-15  Score=110.95  Aligned_cols=75  Identities=27%  Similarity=0.448  Sum_probs=66.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.            |..+.+.  +|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------i~~v~~~--~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   71 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGK------------VLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKLHGVN   71 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSC------------EEEEEEE--TTEEEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhcCCccCCcE
Confidence            45789999999999999999999999997            4444444  799999999999999999 69999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        72 l~v~~a~~~~   81 (90)
T 2dnq_A           72 INVEASKNKS   81 (90)
T ss_dssp             CEEECSSCCC
T ss_pred             EEEEECCCCC
Confidence            9999987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.7e-15  Score=120.00  Aligned_cols=91  Identities=21%  Similarity=0.216  Sum_probs=70.1

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCC--CCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGP--GDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~--~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.....  ..++.+..++.++|||||+|.+.++|.+|+ .||+..|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            4457899999999999999999999999998742100000  001111133556899999999999999999 5999999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|+.|.|.++....
T Consensus        91 ~g~~l~V~~a~~~~  104 (113)
T 2cpe_A           91 QGSKLKVSLARKKP  104 (113)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCCEEEEEECCCCC
Confidence            99999999987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.57  E-value=8.8e-15  Score=114.67  Aligned_cols=85  Identities=19%  Similarity=0.223  Sum_probs=68.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEE-EEecCCCcEEEEEecCHHHHHHHH-Hh-CCcee
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN-VYINHEKKFAFVEMRTVEEASNAM-AL-DGIIF  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~-~~~~~~~g~afv~f~~~~~a~~a~-~l-~~~~~  246 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.+      +.+ ...+.++|||||+|.+.++|.+|+ .| |+..|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~   84 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRL------PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   84 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEE------ecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE
Confidence            3456789999999999999999999999998533211      011 113445899999999999999999 58 99999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|+.|.|.++....
T Consensus        85 ~g~~l~v~~a~~~~   98 (107)
T 2cph_A           85 YGRRLVLEWADSEV   98 (107)
T ss_dssp             SSCBCEEEECCCCC
T ss_pred             CCCEEEEEeCCCCC
Confidence            99999999987654

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.57  E-value=8e-15  Score=112.45  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=66.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      .++|||+|||..+++++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .|+|..|.|+.|.
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   75 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKM------MFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLK   75 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEE------EeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            579999999999999999999999997433111      111112456899999999999999999 6999999999999


Q ss_pred             EcCCCCCCc
Q 013837          253 VRRPTDYNP  261 (435)
Q Consensus       253 v~~~~~~~~  261 (435)
                      |.++.....
T Consensus        76 V~~a~~~~~   84 (96)
T 2x1f_A           76 CGYSSNSDI   84 (96)
T ss_dssp             EEECSCSSG
T ss_pred             EEEcCCCCC
Confidence            999876543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.57  E-value=6.5e-15  Score=117.03  Aligned_cols=82  Identities=21%  Similarity=0.397  Sum_probs=67.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.       +....++.++|||||+|.+.++|.+|+ .|||..|.|+.
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~-------i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~   77 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVL-------LIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA   77 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEE-------EECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE-------EEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4568999999999999999999999999864311       111114567899999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        78 l~V~~a~~~~   87 (116)
T 2fy1_A           78 IKVEQAKKPS   87 (116)
T ss_dssp             CEEEECCCSS
T ss_pred             EEEEECCCCC
Confidence            9999987544

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.57  E-value=4e-15  Score=126.54  Aligned_cols=78  Identities=28%  Similarity=0.597  Sum_probs=73.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+.  ++..+.|+.|.|.++.+
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECCC
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEcccccccc
Confidence            4689999999999999999999999999999999998899999999999999999999998  46899999999999854

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.56  E-value=6.8e-15  Score=115.56  Aligned_cols=86  Identities=10%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceec
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      .+.....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+...+..|.
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i------~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~   92 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV------MRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD   92 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEE------CCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEET
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEE------EECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCC
Confidence            445567899999999999999999999999998533110      01111255689999999999999999976679999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |+.|.|.++...
T Consensus        93 g~~l~V~~a~~~  104 (109)
T 2rs2_A           93 SKTIDPKVAFPR  104 (109)
T ss_dssp             TEEEEEEECCCC
T ss_pred             CEEEEEEEccCC
Confidence            999999987654

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=1.1e-14  Score=114.31  Aligned_cols=76  Identities=25%  Similarity=0.339  Sum_probs=67.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--  248 (435)
                      ...++|||+|||+.+|+++|+++|..||.            |..+.+..+ |||||+|.+.++|.+|| .||+..|.|  
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------i~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   79 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   79 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSC------------EEEEEEETT-TEEEEEESSHHHHHHHHHHSSSEEEECTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EeEEEEecC-CEEEEEECCHHHHHHHHHHHCcCCccCCc
Confidence            45789999999999999999999999997            555555555 99999999999999999 599999999  


Q ss_pred             ---ceEEEcCCCCCC
Q 013837          249 ---VAVRVRRPTDYN  260 (435)
Q Consensus       249 ---~~l~v~~~~~~~  260 (435)
                         +.|.|.++....
T Consensus        80 ~~~~~i~V~~a~~~~   94 (108)
T 1x4c_A           80 GETAYIRVKVDGPRS   94 (108)
T ss_dssp             SCEEEEEEEESSCCS
T ss_pred             CcceEEEEEeCCCCC
Confidence               999999887643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=4.2e-15  Score=115.19  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=67.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ....++|||+|||+.+|+++|.++|+.||.|..+.      ++.+ ..+.++|||||+|.+.++|..|+.+++..|.|+.
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~------i~~d-~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~   80 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ------MRRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETD   80 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEE------EECC-CTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTT
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEE------EEEC-CCCCCccEEEEEECCHHHHHHHHHcCCCEECCEE
Confidence            34568999999999999999999999999854311      0111 1156789999999999999999999999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++.++
T Consensus        81 l~V~~~~~~   89 (103)
T 1s79_A           81 LLILFKDDY   89 (103)
T ss_dssp             CEEEEHHHH
T ss_pred             EEEEEchHH
Confidence            999876544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=6.8e-15  Score=112.40  Aligned_cols=75  Identities=23%  Similarity=0.301  Sum_probs=65.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe------cCCCcEEEEEecCHHHHHHHH-HhCC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI------NHEKKFAFVEMRTVEEASNAM-ALDG  243 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~------~~~~g~afv~f~~~~~a~~a~-~l~~  243 (435)
                      ....++|||+|||..+++++|+++|..||.|            ..+.+      +.++|||||+|.+.++|.+|+ .||+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v------------~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g   80 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKV------------VKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINN   80 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCE------------EEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCe------------EEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCC
Confidence            3467899999999999999999999999974            33433      456899999999999999999 6999


Q ss_pred             ceecCceEEEcCCC
Q 013837          244 IIFEGVAVRVRRPT  257 (435)
Q Consensus       244 ~~~~g~~l~v~~~~  257 (435)
                      ..|.|+.|.|.+++
T Consensus        81 ~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           81 KQLFGRVIKASIAI   94 (94)
T ss_dssp             EEETTEEEEEEECC
T ss_pred             CeeCCcEEEEEecC
Confidence            99999999998763

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.7e-15  Score=117.89  Aligned_cols=84  Identities=20%  Similarity=0.325  Sum_probs=69.2

Q ss_pred             hhhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       168 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .......++|||+|||..+|+++|+++|..||.|..+.        +....+.++|||||+|.+.++|.+|+ .|+|..|
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~--------i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~   94 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVE--------IIFNERGSKGFGFVTFENSADADRAREKLHGTVV   94 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEE--------ECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEE
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEE--------EEECCCCCceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            34556789999999999999999999999999864421        11112346899999999999999999 5999999


Q ss_pred             cCceEEEcCCCCC
Q 013837          247 EGVAVRVRRPTDY  259 (435)
Q Consensus       247 ~g~~l~v~~~~~~  259 (435)
                      +|+.|.|.++...
T Consensus        95 ~g~~l~V~~a~~~  107 (109)
T 2err_A           95 EGRKIEVNNATAR  107 (109)
T ss_dssp             TTEECEEEECCCS
T ss_pred             CCEEEEEEECCCC
Confidence            9999999987643

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.56  E-value=8.9e-16  Score=116.06  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=67.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+.+++..|.|+.|
T Consensus         4 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l   77 (89)
T 3ucg_A            4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVT------ILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQI   77 (89)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEE------EEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEEC
T ss_pred             CcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEE
Confidence            3568999999999999999999999999864311      0111124566899999999999999999999999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        78 ~V~~a~~~   85 (89)
T 3ucg_A           78 KVIPKRTN   85 (89)
T ss_dssp             EEEETTTT
T ss_pred             EEEEccCC
Confidence            99987643

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=6.8e-15  Score=113.32  Aligned_cols=82  Identities=21%  Similarity=0.280  Sum_probs=67.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~---~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      +.++|||+|||+.+|+++|+++|..||.|..+.      .+.+..   ++.++|||||+|.+.++|.+|+ .||+..|.|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT------ISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG   77 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            568999999999999999999999999864421      011111   2256799999999999999999 499999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        78 ~~l~V~~a~~~~   89 (98)
T 2cpf_A           78 HKLEVRISERAT   89 (98)
T ss_dssp             EECEEECSSCSS
T ss_pred             eEEEEEEccCCC
Confidence            999999987654

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.56  E-value=1.8e-15  Score=115.81  Aligned_cols=79  Identities=18%  Similarity=0.179  Sum_probs=67.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+.+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.|
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l   87 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSV------CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCC------EEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceE------EEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            458999999999999999999999999875432      2333344567899999999999999999 599999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      .|.++.
T Consensus        88 ~v~~a~   93 (95)
T 2ek1_A           88 KLSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEecc
Confidence            999764

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.5e-14  Score=109.44  Aligned_cols=76  Identities=22%  Similarity=0.416  Sum_probs=66.8

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.            |..+.+.  ++||||+|.+.++|.+|+ .||+..|.|+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~   71 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGR------------VIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVKGK   71 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCC------------EEEEEEE--CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            346789999999999999999999999997            5555554  569999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        72 ~l~v~~a~~~~   82 (90)
T 2dnp_A           72 RINVELSTKGQ   82 (90)
T ss_dssp             ECEEEESCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987553

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.56  E-value=9.3e-16  Score=118.43  Aligned_cols=83  Identities=23%  Similarity=0.358  Sum_probs=65.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE----ecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY----INHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~----~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      ...++|||+|||..+|+++|+++|..||.|......  +..++.+.    ++.++|||||+|.+.++|.+|+ .|||..|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~--~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKT--GQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTT--TEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeecccc--ccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            456899999999999999999999999986430000  00002222    3456899999999999999999 5999999


Q ss_pred             cCceEEEcCC
Q 013837          247 EGVAVRVRRP  256 (435)
Q Consensus       247 ~g~~l~v~~~  256 (435)
                      .|+.|.|.++
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999999876

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.56  E-value=5.6e-15  Score=111.08  Aligned_cols=81  Identities=11%  Similarity=0.314  Sum_probs=65.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+++++..|.|+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~   80 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCT------IKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGR   80 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEE------EEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEE------EeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCE
Confidence            445778999999999999999999999999854311      01111235568999999999999999999899999999


Q ss_pred             eEEEcCC
Q 013837          250 AVRVRRP  256 (435)
Q Consensus       250 ~l~v~~~  256 (435)
                      .|.|.++
T Consensus        81 ~i~v~~A   87 (87)
T 3s7r_A           81 VIDPKKA   87 (87)
T ss_dssp             EEEEEEC
T ss_pred             EEEEEeC
Confidence            9999864

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.6e-15  Score=117.15  Aligned_cols=83  Identities=18%  Similarity=0.333  Sum_probs=67.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhh-cCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAI-GGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~-~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g  248 (435)
                      ....++|||+|||+.+|+++|+++|..||.|. .+.      ++.+..++.++|||||+|.+.++|.+|++ ||+..|.|
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   79 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVK------IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG   79 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEE------EEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEE------EeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            34678999999999999999999999999864 311      11111234567999999999999999995 99999999


Q ss_pred             ce----EEEcCCCCC
Q 013837          249 VA----VRVRRPTDY  259 (435)
Q Consensus       249 ~~----l~v~~~~~~  259 (435)
                      +.    |.|.++...
T Consensus        80 ~~~~~~l~v~~a~~~   94 (99)
T 2div_A           80 ATPAKRFKLNYATYS   94 (99)
T ss_dssp             CSSCEECCEEETTCC
T ss_pred             CCcceeEEEeecCCC
Confidence            99    999987654

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=2.9e-15  Score=116.92  Aligned_cols=78  Identities=23%  Similarity=0.312  Sum_probs=67.0

Q ss_pred             cccCCeEEEcCCCCC-CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC--Ccee
Q 013837          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIF  246 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~--~~~~  246 (435)
                      ..+.++|||+|||+. +|+++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .|+  +..|
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~------------V~~v~i~~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l   89 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF   89 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCHHHHHHHHHHhccCCceE
Confidence            346789999999998 999999999999998            445555678999999999999999999 464  5679


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|++|.|.++....
T Consensus        90 ~Gr~l~V~~a~~~~  103 (112)
T 1x4f_A           90 QGRCVKVDLSEKYK  103 (112)
T ss_dssp             SSSCCEEEEECSCS
T ss_pred             CCEEEEEEECcccc
Confidence            99999999986543

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.56  E-value=1.3e-14  Score=112.00  Aligned_cols=83  Identities=24%  Similarity=0.310  Sum_probs=67.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .||+..|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   79 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHY------PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRM   79 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEE------EecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            46789999999999999999999999997433111      011113456799999999999999999 79999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        80 l~V~~a~~~~   89 (99)
T 1whw_A           80 LHVLPSTIKK   89 (99)
T ss_dssp             EEEEECCCCS
T ss_pred             EEEEEcCCCc
Confidence            9999987654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=9.5e-15  Score=111.80  Aligned_cols=82  Identities=21%  Similarity=0.257  Sum_probs=67.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      .+++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .||+..|.|++|
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   77 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIV------LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM   77 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE------EECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE------EeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEE
Confidence            568999999999999999999999999854311      0111113556899999999999999999 499999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++....
T Consensus        78 ~V~~a~~~~   86 (95)
T 2dnz_A           78 RVGHVTERL   86 (95)
T ss_dssp             EEEESSCCC
T ss_pred             EEEEccccc
Confidence            999987654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.55  E-value=2.9e-15  Score=117.19  Aligned_cols=85  Identities=16%  Similarity=0.229  Sum_probs=69.1

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee--
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~--  246 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..+  
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~   82 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTV------LKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLP   82 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEEC------CCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEE------EecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccC
Confidence            3456789999999999999999999999998644211      111123567899999999999999999 5999987  


Q ss_pred             -cCceEEEcCCCCCC
Q 013837          247 -EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 -~g~~l~v~~~~~~~  260 (435)
                       .|++|.|.++....
T Consensus        83 ~~g~~l~v~~a~~~~   97 (106)
T 2dgp_A           83 GMNRPIQVKPADSES   97 (106)
T ss_dssp             TCSSCCEEEECCCCS
T ss_pred             CCCceEEEEECCccc
Confidence             89999999887543

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.55  E-value=7.9e-15  Score=109.21  Aligned_cols=79  Identities=18%  Similarity=0.415  Sum_probs=64.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      .+|||+|||..+++++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|+.|.|
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~------i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   75 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGH------VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI   75 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEE------EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE------EEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEE
Confidence            5899999999999999999999999854310      0111123455899999999999999999 59999999999999


Q ss_pred             cCCCCC
Q 013837          254 RRPTDY  259 (435)
Q Consensus       254 ~~~~~~  259 (435)
                      .++.+.
T Consensus        76 ~~a~~~   81 (83)
T 3md1_A           76 NWAAKL   81 (83)
T ss_dssp             EECCCC
T ss_pred             EecCcC
Confidence            988654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.55  E-value=1.3e-14  Score=115.91  Aligned_cols=81  Identities=17%  Similarity=0.268  Sum_probs=65.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .|||..|.|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i------~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  109 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV------FIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGT  109 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEE------CCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3456789999999999999999999999998533110      111123456899999999999999999 599999999


Q ss_pred             ceEEEcCC
Q 013837          249 VAVRVRRP  256 (435)
Q Consensus       249 ~~l~v~~~  256 (435)
                      +.|.|.++
T Consensus       110 ~~l~V~~a  117 (118)
T 2khc_A          110 KRLKVQLK  117 (118)
T ss_dssp             EECCEEEC
T ss_pred             EEEEEEec
Confidence            99999875

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.55  E-value=3.5e-14  Score=121.46  Aligned_cols=80  Identities=15%  Similarity=0.164  Sum_probs=66.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+++++|+++|..||.|..+.+      +.+ ..+.++|||||+|.+.++|.+|+ .||+..|.|++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i------~~d-~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~  158 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV------DYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRP  158 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEE------CCC-TTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EEC-CCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEE
Confidence            35689999999999999999999999998643211      111 13567899999999999999999 59999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.++..
T Consensus       159 l~V~~a~~  166 (177)
T 2f3j_A          159 MDIQLVAS  166 (177)
T ss_dssp             CEEEEESS
T ss_pred             EEEEEecC
Confidence            99998764

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.55  E-value=3.4e-15  Score=113.55  Aligned_cols=80  Identities=18%  Similarity=0.219  Sum_probs=67.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+        .+....+.++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~--------~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~   77 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYA--------DIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE   77 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEE--------EEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEE--------EEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            467899999999999999999999999986431        111124456899999999999999999 59999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++...
T Consensus        78 l~v~~a~~~   86 (92)
T 2dgv_A           78 IDVRIDRNA   86 (92)
T ss_dssp             CCCEECSCC
T ss_pred             EEEEEcCCC
Confidence            999987654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.4e-15  Score=122.57  Aligned_cols=81  Identities=19%  Similarity=0.190  Sum_probs=69.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+||.+|+..|.|+.|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~------~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i   96 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI------YIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI   96 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTC------EEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCB
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceE------EEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEE
Confidence            4568999999999999999999999999875421      2334446677899999999999999999999999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        97 ~V~~a~~  103 (124)
T 1wel_A           97 QVHPITK  103 (124)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9998754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=2.2e-15  Score=120.00  Aligned_cols=85  Identities=19%  Similarity=0.329  Sum_probs=68.8

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+||..++..|.|+
T Consensus        23 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~   96 (116)
T 1x4b_A           23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV------VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGR   96 (116)
T ss_dssp             HHHHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE------EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCE
Confidence            345668999999999999999999999999864311      01111235578999999999999999997799999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        97 ~l~V~~a~~~~  107 (116)
T 1x4b_A           97 VVEPKRAVARE  107 (116)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEEEECCCCc
Confidence            99999987653

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.55  E-value=3.9e-16  Score=120.76  Aligned_cols=84  Identities=17%  Similarity=0.227  Sum_probs=65.6

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCcEEEEEecCHHHHHHHHHhCCceec
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~-~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      ......++|||+|||..+|+++|+++|..|| |..+.+      +.+. ..+.++|||||+|.+.++|.+|+.|+|..|.
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i------~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~   86 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL------PREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLG   86 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEEC------SCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBT
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE------EecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEEC
Confidence            3445679999999999999999999999998 654221      1111 2455789999999999999999999999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |+.|.|.++...
T Consensus        87 g~~l~V~~a~~~   98 (100)
T 2j76_E           87 NRRIRVDVADQA   98 (100)
T ss_dssp             TBCCCCEECCCS
T ss_pred             CeEEEEEeccCC
Confidence            999999987653

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.55  E-value=1.7e-14  Score=114.66  Aligned_cols=86  Identities=23%  Similarity=0.339  Sum_probs=68.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.      ++.+...+.++|||||+|.+.++|.+|+ .|++..|.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDAR------VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   84 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            345678999999999999999999999999854310      0011113445799999999999999999 599999999


Q ss_pred             ceEEEcCCCCCCc
Q 013837          249 VAVRVRRPTDYNP  261 (435)
Q Consensus       249 ~~l~v~~~~~~~~  261 (435)
                      +.|.|.++.....
T Consensus        85 ~~l~V~~a~~~~~   97 (115)
T 2dgo_A           85 RQIRTNWATRKPP   97 (115)
T ss_dssp             EECEEEESSCCCC
T ss_pred             EEEEEEEccCCCC
Confidence            9999999876543

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=99.55  E-value=3.2e-14  Score=110.54  Aligned_cols=75  Identities=21%  Similarity=0.317  Sum_probs=66.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.            |..+.+.  ++||||+|.+.++|.+|+ .|++..|.|+.
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~~   74 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGK------------LERVKKL--KDYAFIHFDERDGAVKAMEEMNGKDLEGEN   74 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSC------------EEEEEEC--SSCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCC------------EEEEEEE--CCEEEEEeCCHHHHHHHHHHHCCCccCCCE
Confidence            45689999999999999999999999997            4555553  679999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        75 l~v~~a~~~~   84 (103)
T 2dgu_A           75 IEIVFAKPPD   84 (103)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEcCCCc
Confidence            9999987654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.55  E-value=8.7e-15  Score=112.02  Aligned_cols=76  Identities=32%  Similarity=0.468  Sum_probs=65.8

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEecCHHHHHHHHH-hCC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMA-LDG  243 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-----~~~~g~afv~f~~~~~a~~a~~-l~~  243 (435)
                      .....++|||+|||+.+++++|+++|..||.|.            .+.+     +.++|||||+|.+.++|.+|++ ||+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~------------~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g   79 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLT------------KVTICKDREGKPKSFGFVCFKHPESVSYAIALLNG   79 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEE------------EEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEE------------EEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCC
Confidence            345678999999999999999999999999853            3332     3457999999999999999995 999


Q ss_pred             ceecCceEEEcCCC
Q 013837          244 IIFEGVAVRVRRPT  257 (435)
Q Consensus       244 ~~~~g~~l~v~~~~  257 (435)
                      ..|.|+.|.|.++.
T Consensus        80 ~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           80 IRLYGRPINVSGPS   93 (95)
T ss_dssp             CEETTEECEEECCC
T ss_pred             CEECCCEEEEEEcC
Confidence            99999999999875

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.55  E-value=1.9e-15  Score=110.24  Aligned_cols=75  Identities=17%  Similarity=0.276  Sum_probs=63.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      +|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+++++..+.|+.|.|.+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~   74 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIEL------PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECC------CCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            5999999999999999999999998755322      2223346779999999999999999998899999999999875


Q ss_pred             C
Q 013837          256 P  256 (435)
Q Consensus       256 ~  256 (435)
                      +
T Consensus        75 a   75 (75)
T 1iqt_A           75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.55  E-value=8.5e-16  Score=118.76  Aligned_cols=80  Identities=18%  Similarity=0.271  Sum_probs=66.8

Q ss_pred             cCCeEEEcCCCC------CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          173 HARRVYVGGLPP------LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       173 ~~~~l~V~nlp~------~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      ..++|||+|||.      .+++++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .|||..
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~------i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~   78 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNME------FPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKR   78 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEE------CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEE------EEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcc
Confidence            467999999999      999999999999999864421      1222233667899999999999999999 699999


Q ss_pred             ecC-ceEEEcCCCC
Q 013837          246 FEG-VAVRVRRPTD  258 (435)
Q Consensus       246 ~~g-~~l~v~~~~~  258 (435)
                      |.| +.|.|.++.+
T Consensus        79 ~~g~r~l~V~~a~~   92 (100)
T 3ns6_A           79 LDLKHRLFLYTMKD   92 (100)
T ss_dssp             SSSSCBCEEEESHH
T ss_pred             cCCCeEEEEEECch
Confidence            999 9999998753

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-15  Score=118.85  Aligned_cols=83  Identities=20%  Similarity=0.307  Sum_probs=67.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|+|..|.|+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~   96 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQ------LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGR   96 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEE------EEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            45678999999999999999999999999854310      0111112456799999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++.+.
T Consensus        97 ~l~V~~a~~k  106 (108)
T 2jrs_A           97 PMKVGHVTER  106 (108)
T ss_dssp             CCEEECSCSS
T ss_pred             EEEEEEcccC
Confidence            9999987653

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=5.6e-15  Score=114.91  Aligned_cols=84  Identities=18%  Similarity=0.173  Sum_probs=68.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|++ ||+..|.|+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYI------PREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGR   83 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEC------CBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTB
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            346789999999999999999999999997533111      1111125568999999999999999995 999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2dnm_A           84 ELRVQVARYGR   94 (103)
T ss_dssp             CCEEEECSSCC
T ss_pred             EEEEEECCcCC
Confidence            99999987543

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=6.4e-15  Score=116.87  Aligned_cols=83  Identities=23%  Similarity=0.308  Sum_probs=67.6

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+||.||+..|.|+
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~   94 (114)
T 2cq4_A           21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRI------ISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGV   94 (114)
T ss_dssp             THHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEE------CCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEE------EecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCe
Confidence            3456789999999999999999999999997533110      1111225678999999999999999999999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .|.|.++..
T Consensus        95 ~l~V~~a~~  103 (114)
T 2cq4_A           95 PIIVQASQA  103 (114)
T ss_dssp             EEEEEEHHH
T ss_pred             EEEEEecCC
Confidence            999997653

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.54  E-value=1.2e-14  Score=109.57  Aligned_cols=80  Identities=23%  Similarity=0.292  Sum_probs=64.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHHH-hCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAMA-LDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~  250 (435)
                      ..++|||+|||..+|+++|+++|..||.|..+.+      +.+..++. ++|||||+|.+.++|.+|+. |||..|.|+.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i------~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   76 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDM------PVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE   76 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEE------EeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeE
Confidence            4679999999999999999999999998533110      11111122 78999999999999999995 9999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.++.+
T Consensus        77 l~v~~a~~   84 (88)
T 4a8x_A           77 ITATAVLA   84 (88)
T ss_dssp             CEEEEECC
T ss_pred             EEEEECCC
Confidence            99998754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.54  E-value=1.4e-14  Score=129.85  Aligned_cols=78  Identities=18%  Similarity=0.290  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+.++|||+|||. .+|+++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+||+.|||..|.|+.|.|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4568999999999 99999999999999999999999874     78999999999999999999999999999999999


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      +...
T Consensus       107 a~~~  110 (229)
T 2adc_A          107 SKHQ  110 (229)
T ss_dssp             CSCC
T ss_pred             ecCc
Confidence            9765

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=6.8e-15  Score=114.43  Aligned_cols=82  Identities=22%  Similarity=0.257  Sum_probs=68.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.|..+.        +....+.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~--------i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   83 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAK--------VMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATK   83 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEE--------EEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE--------EEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            34678999999999999999999999999864321        11114467899999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        84 ~l~V~~a~~~~   94 (103)
T 2d9p_A           84 PLYVALAQRKE   94 (103)
T ss_dssp             BCEEEECSSCC
T ss_pred             EEEEEEecccc
Confidence            99999987654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.1e-15  Score=118.90  Aligned_cols=84  Identities=15%  Similarity=0.228  Sum_probs=68.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIY------LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL   85 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE------EeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCc
Confidence            45678999999999999999999999999854311      0111123456799999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        86 ~l~v~~a~~~~   96 (103)
T 2cq0_A           86 ILNVEWAKPST   96 (103)
T ss_dssp             ECEEEESSCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987553

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.54  E-value=8.1e-15  Score=110.20  Aligned_cols=80  Identities=25%  Similarity=0.346  Sum_probs=64.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .||+..|.|+.|
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   78 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDAR------VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   78 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            567999999999999999999999999854310      0011113446799999999999999999 599999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        79 ~v~~a~~   85 (87)
T 3bs9_A           79 RTNWATR   85 (87)
T ss_dssp             EEEEEC-
T ss_pred             EEEecCC
Confidence            9998754

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=6.9e-15  Score=115.04  Aligned_cols=83  Identities=22%  Similarity=0.194  Sum_probs=66.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|||..|.|+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   93 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIH------LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   93 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEE------EEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            34568999999999999999999999999853310      0011112456899999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        94 ~l~V~~a~~~  103 (106)
T 1p27_B           94 PISVDWCFVR  103 (106)
T ss_dssp             BCEEEESEES
T ss_pred             EEEEEeecCC
Confidence            9999987543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.1e-14  Score=113.08  Aligned_cols=84  Identities=25%  Similarity=0.413  Sum_probs=68.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV------VKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGR   82 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEE------CCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEE------EeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            346789999999999999999999999998543110      111113456899999999999999999 6999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        83 ~l~v~~a~~~~   93 (102)
T 1x5s_A           83 QIRVDQAGKSS   93 (102)
T ss_dssp             CCEEEEEECCC
T ss_pred             EEEEEECCCCC
Confidence            99999876543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.4e-14  Score=111.97  Aligned_cols=83  Identities=18%  Similarity=0.287  Sum_probs=67.5

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.       +.....+.++|||||+|.+.++|.+|+ .||+..|.|
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~-------i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   85 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLR-------LVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKE   85 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEE-------EEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE-------EEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            345678999999999999999999999999854311       111112456799999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++.+.
T Consensus        86 ~~l~v~~a~~~   96 (100)
T 2do4_A           86 NIIKVAISNSG   96 (100)
T ss_dssp             CEEEEEECCCC
T ss_pred             EEEEEEECCCC
Confidence            99999987654

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=2.1e-14  Score=113.27  Aligned_cols=84  Identities=20%  Similarity=0.280  Sum_probs=68.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC------C
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD------G  243 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~------~  243 (435)
                      ....++|||+|||+.+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|| .++      +
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~   85 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGG   85 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCC
Confidence            346789999999999999999999999997533211      111123457899999999999999999 599      9


Q ss_pred             ceecCceEEEcCCCCCC
Q 013837          244 IIFEGVAVRVRRPTDYN  260 (435)
Q Consensus       244 ~~~~g~~l~v~~~~~~~  260 (435)
                      ..|.|+.|.|.++....
T Consensus        86 ~~~~g~~l~v~~a~~~~  102 (111)
T 1x4h_A           86 LKLDGRQLKVDLAVTRD  102 (111)
T ss_dssp             EESSSCEEEEECCCCCC
T ss_pred             cEEcCEEEEEEECCCCc
Confidence            99999999999987653

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=99.54  E-value=3.5e-15  Score=115.78  Aligned_cols=72  Identities=13%  Similarity=0.259  Sum_probs=62.4

Q ss_pred             EcCCCCCCCHHHHHHHH------------HhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          299 VGGLPYYFTETQIKELL------------ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       299 V~nLp~~~te~~l~~~F------------~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      +.||+..+++++|++.|            ++||.|..|.|+.+. ++.++|||||+|.+.++|.+|+..|||..|+|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            45566666776666555            999999999999886 47899999999999999999999999999999999


Q ss_pred             EEEEc
Q 013837          367 TVRRA  371 (435)
Q Consensus       367 ~V~~a  371 (435)
                      .|.|+
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99997

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=3.9e-15  Score=115.36  Aligned_cols=81  Identities=20%  Similarity=0.274  Sum_probs=69.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|.         .+.+ ..+.++|||||+|.+.++|.+|+. ||+..|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~---------~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   80 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFIK---------VPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEG   80 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEEE---------CCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEEE---------EEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            345678999999999999999999999999751         1222 456789999999999999999995 99999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        81 ~~l~v~~a~~~~   92 (101)
T 2fc9_A           81 RAIRLELQGPRG   92 (101)
T ss_dssp             EEEEEEECSSCC
T ss_pred             eEEEEEEcCCCC
Confidence            999999987543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.54  E-value=2.5e-15  Score=125.73  Aligned_cols=81  Identities=20%  Similarity=0.251  Sum_probs=65.0

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ...++|||+|||+.+|+++|+++|..||  .|..+.      ++.+..++.++|||||+|.+.++|.+|| .|||..|.|
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~------i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~G  126 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELK------FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG  126 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEE------EEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4568999999999999999999999999  643311      1111124567899999999999999999 589999999


Q ss_pred             ceEEEcCCCC
Q 013837          249 VAVRVRRPTD  258 (435)
Q Consensus       249 ~~l~v~~~~~  258 (435)
                      +.|.|.++..
T Consensus       127 r~l~V~~a~~  136 (156)
T 3n9u_C          127 EKVDVRPATR  136 (156)
T ss_dssp             EECEEEECCH
T ss_pred             eEeEEEEcCC
Confidence            9999998764

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.7e-15  Score=118.32  Aligned_cols=85  Identities=16%  Similarity=0.292  Sum_probs=68.5

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+||..++..|.|+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~   85 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCV------IMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGR   85 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEE------EEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCE
Confidence            345678999999999999999999999999864311      01111234567999999999999999996699999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        86 ~l~V~~a~~~~   96 (105)
T 2dh8_A           86 NIDPKPCTPRG   96 (105)
T ss_dssp             EEBCCCSCCSS
T ss_pred             EEEEEEccCCC
Confidence            99999987554

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.54  E-value=1.9e-14  Score=109.37  Aligned_cols=76  Identities=26%  Similarity=0.433  Sum_probs=66.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|            ..+.+.  ++||||+|.+.++|.+|+ .||+..|.|+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v------------~~v~~~--~~~afV~f~~~~~a~~A~~~l~g~~~~g~   72 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPV------------IECDIV--KDYAFVHMERAEDAVEAIRGLDNTEFQGK   72 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCC------------CEEEEC--SSEEEEEESCHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCe------------EEEEEE--CCEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            4567899999999999999999999999974            344443  569999999999999999 6999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        73 ~l~V~~a~~~~   83 (92)
T 2dgt_A           73 RMHVQLSTSRL   83 (92)
T ss_dssp             EEEEEESSCCC
T ss_pred             EEEEEEccCCC
Confidence            99999987553

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.6e-14  Score=112.77  Aligned_cols=76  Identities=18%  Similarity=0.279  Sum_probs=66.7

Q ss_pred             ccCCeEEE--cCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee--
Q 013837          172 RHARRVYV--GGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--  246 (435)
Q Consensus       172 ~~~~~l~V--~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~--  246 (435)
                      .+.++|||  +||++.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|||..|  
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~------------v~~v~i~~~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            35678999  779999999999999999997            566666678999999999999999999 6999988  


Q ss_pred             ---cCceEEEcCCCCC
Q 013837          247 ---EGVAVRVRRPTDY  259 (435)
Q Consensus       247 ---~g~~l~v~~~~~~  259 (435)
                         .|++|.|.++...
T Consensus        91 ~lg~g~~l~v~~a~~~  106 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKV  106 (114)
T ss_dssp             TTSCEEECEEEEESCC
T ss_pred             ccCCCcEEEEEecccC
Confidence               6889999987644

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=1.9e-15  Score=119.87  Aligned_cols=83  Identities=12%  Similarity=0.099  Sum_probs=68.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHh-hcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTA-IGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i-~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.| ..+.      ++.+. ++.++|||||+|.+.++|.+||++++..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~------i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr   84 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVH------VLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGR   84 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEE------ECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEE------EEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCe
Confidence            3467899999999999999999999999875 3311      11122 56789999999999999999997799999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        85 ~i~v~~a~~~~   95 (114)
T 2cpy_A           85 EAFVHVVTLED   95 (114)
T ss_dssp             EEEEEEECHHH
T ss_pred             EEEEEECCHHH
Confidence            99999876543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.3e-15  Score=117.37  Aligned_cols=82  Identities=17%  Similarity=0.239  Sum_probs=67.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-cCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..|| |..+.+      +.+..+ +.++|||||+|.+.++|.+||.|++..|.|+.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i------~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~   85 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRL------PREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKR   85 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEEC------CBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEE------ecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcE
Confidence            3568999999999999999999999998 644211      111122 56789999999999999999999999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        86 l~V~~a~~~~   95 (104)
T 1wi8_A           86 IRVDVADQAQ   95 (104)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEccCCC
Confidence            9999887643

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.54  E-value=1.2e-14  Score=113.46  Aligned_cols=83  Identities=22%  Similarity=0.217  Sum_probs=67.5

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC-
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG-  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g-  248 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.       +.....+.++|||||+|.+.++|.+|+ .||+..|.| 
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~-------i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg   84 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECT-------VLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG   84 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEE-------EEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE-------EEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCC
Confidence            34678999999999999999999999999864321       111113445899999999999999999 599999998 


Q ss_pred             --ceEEEcCCCCCC
Q 013837          249 --VAVRVRRPTDYN  260 (435)
Q Consensus       249 --~~l~v~~~~~~~  260 (435)
                        ++|.|.++....
T Consensus        85 ~~~~l~V~~a~~~~   98 (105)
T 2dnh_A           85 ASSSLVVKFADTDK   98 (105)
T ss_dssp             CSSCCEEEESCSSC
T ss_pred             CCccEEEEECccCc
Confidence              999999887543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.54  E-value=3.6e-15  Score=118.86  Aligned_cols=81  Identities=17%  Similarity=0.194  Sum_probs=67.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      ....++|||+|||+.+|+++|+++|..||.   |..+.       +.....+.++|||||+|.+.++|.+||++++..|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~-------i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~   86 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVH-------FIYTREGRQSGEAFVELESEDDVKLALKKDRESMG   86 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEE-------EEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEET
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEE-------EEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeEC
Confidence            456789999999999999999999999998   44311       11112356789999999999999999999999999


Q ss_pred             CceEEEcCCCC
Q 013837          248 GVAVRVRRPTD  258 (435)
Q Consensus       248 g~~l~v~~~~~  258 (435)
                      |+.|.|.++..
T Consensus        87 gr~i~V~~a~~   97 (118)
T 2db1_A           87 HRYIEVFKSHR   97 (118)
T ss_dssp             TEEEEEEEECH
T ss_pred             CeEEEEEECCH
Confidence            99999987753

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A

Probab=99.53  E-value=1.1e-14  Score=117.77  Aligned_cols=83  Identities=22%  Similarity=0.259  Sum_probs=67.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++..+|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVS------IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEE------EECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            35678999999999999999999999999853311      0011123467899999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      +|.|.++...
T Consensus       117 ~l~V~~a~~~  126 (129)
T 2kxn_B          117 RIRVDFSITK  126 (129)
T ss_dssp             CCEESCCSSS
T ss_pred             EEEEEEecCC
Confidence            9999998654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.53  E-value=5.6e-15  Score=113.32  Aligned_cols=79  Identities=18%  Similarity=0.252  Sum_probs=69.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..         +  ...+.++|||||+|.+.++|.+|+. |+|..|.|
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~---------~--~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   80 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRL---------V--SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECC---------E--EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEE---------e--CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456789999999999999999999999998621         3  5566788999999999999999995 99999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++.+.
T Consensus        81 ~~l~v~~a~~~   91 (96)
T 1fjc_A           81 RSVSLYYTGEK   91 (96)
T ss_dssp             EEEEEEECSSS
T ss_pred             eEEEEEEcCCC
Confidence            99999987654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.53  E-value=3.7e-15  Score=121.28  Aligned_cols=86  Identities=15%  Similarity=0.278  Sum_probs=70.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc----
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI----  244 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~----  244 (435)
                      .....++|||+|||+.+|+++|+++|..||.|....    ..++.+..++.++|||||+|.+. +|.+|+ .||+.    
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~----v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~   93 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSN----VRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPL   93 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTT----EECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceee----EEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCc
Confidence            345678999999999999999999999999874310    01233344677899999999999 999999 69999    


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|.|+.|.|.++....
T Consensus        94 ~~~gr~l~V~~a~~~~  109 (131)
T 2m2b_A           94 TIDGKTINVEFAKGSK  109 (131)
T ss_dssp             CGGGCCCCCEECCCSC
T ss_pred             cCCCEEEEEEECCCCC
Confidence            9999999999887653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=2.1e-15  Score=117.30  Aligned_cols=82  Identities=22%  Similarity=0.321  Sum_probs=66.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..|| |..+.      ++.+..++.++|||||+|.+.++|.+||.||+..|.|+.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l   85 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVR------LVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSL   85 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEE------EeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEE
Confidence            4578999999999999999999999996 53311      0111123456899999999999999999999999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++....
T Consensus        86 ~V~~a~~~~   94 (103)
T 2dng_A           86 RVDIAEGRK   94 (103)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEecCCC
Confidence            999887543

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.53  E-value=5.9e-15  Score=112.49  Aligned_cols=77  Identities=21%  Similarity=0.389  Sum_probs=65.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCC-ceecCc
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG-IIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~-~~~~g~  249 (435)
                      ...++|||+|||..+|+++|+++|..||.|+..        +..    .++|||||+|.+.++|.+|+ .||+ ..|.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~--------~~~----~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~   73 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAG--------QVL----LKSGYAFVDYPDQNWAIRAIETLSGKVELHGK   73 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSS--------CEE----EETTEEEECCSCHHHHHHHHHHHTTTCEETTE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEE--------EEE----cCCCEEEEEECCHHHHHHHHHHccCCeeECCE
Confidence            356899999999999999999999999984321        111    25899999999999999999 5999 999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        74 ~l~v~~a~~~~   84 (93)
T 2cqh_A           74 IMEVDYSVSKK   84 (93)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999987543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.52  E-value=1.6e-14  Score=119.49  Aligned_cols=88  Identities=16%  Similarity=0.183  Sum_probs=71.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.+. ..-.+....++.++|||||+|.+.++|.+|+ .|||..|.|+.
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~-~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQR-IMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHH-HHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccc-ceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            456899999999999999999999999987431000 0001333467889999999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999986543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.9e-14  Score=108.24  Aligned_cols=76  Identities=22%  Similarity=0.349  Sum_probs=68.0

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+||  .+|+++|+++|..||.            |..+.+..++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~------------i~~v~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   77 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESV   77 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCC------------EEEEEecCCCCEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            346789999996  8999999999999997            666777889999999999999999999 6999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        78 ~l~v~~a~~~~   88 (97)
T 1x5p_A           78 QLKVNIARKQP   88 (97)
T ss_dssp             EEEEECCSSCC
T ss_pred             EEEEEECCCCC
Confidence            99999986543

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=1.9e-15  Score=117.85  Aligned_cols=85  Identities=31%  Similarity=0.434  Sum_probs=68.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+++++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .|||..|.|+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE------EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEE------EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            34568999999999999999999999999864311      0111113456899999999999999999 5999999999


Q ss_pred             eEEEcCCCCCCc
Q 013837          250 AVRVRRPTDYNP  261 (435)
Q Consensus       250 ~l~v~~~~~~~~  261 (435)
                      .|.|.++.....
T Consensus        79 ~l~v~~a~~~~~   90 (104)
T 1p1t_A           79 ALRVDNAASEKN   90 (104)
T ss_dssp             CBEEEETTCTTH
T ss_pred             EEEEEeCCCccc
Confidence            999999876554

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.52  E-value=5.5e-15  Score=112.17  Aligned_cols=80  Identities=19%  Similarity=0.268  Sum_probs=66.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..| .|..+.      .+.+ ..+.++|||||+|.+.++|.+|+.+|+..|.|+.|
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~------i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i   79 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIR------IVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYI   79 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEE------EEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEE------EEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEE
Confidence            457899999999999999999999999 654311      1111 23556899999999999999999999999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        80 ~v~~a~~~   87 (91)
T 2dgw_A           80 EVFREKSG   87 (91)
T ss_dssp             EEEEESSC
T ss_pred             EEEECCcC
Confidence            99987654

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.52  E-value=7.3e-15  Score=125.98  Aligned_cols=83  Identities=18%  Similarity=0.308  Sum_probs=72.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|..||.|.. .++.+..+|.++|||||+|.+.++|.+||+ |||..|.|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEec
Confidence            455689999999999999999999999998766 234444578899999999999999999995 999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      +..+.
T Consensus        88 ~~~~~   92 (175)
T 1fje_B           88 PKGRD   92 (175)
T ss_dssp             CCCSS
T ss_pred             CCCcc
Confidence            97654

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=4.1e-15  Score=115.84  Aligned_cols=80  Identities=19%  Similarity=0.199  Sum_probs=66.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhc-CCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIG-GNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~-~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|.. +.      ++.+ .++.++|||||+|.+.++|.+||..++..|+|+.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~------i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~   85 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMT------LPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRY   85 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEE------CCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEE------EEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcE
Confidence            45689999999999999999999999997532 10      0111 3567789999999999999999977999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.++..
T Consensus        86 i~v~~~~~   93 (104)
T 1wg5_A           86 IEIFKSSR   93 (104)
T ss_dssp             CEEEEECT
T ss_pred             EEEEECCH
Confidence            99987654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.51  E-value=2.1e-14  Score=111.96  Aligned_cols=82  Identities=20%  Similarity=0.244  Sum_probs=67.9

Q ss_pred             cccCCeEEEcCCCCCC------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCC
Q 013837          171 TRHARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDG  243 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~  243 (435)
                      ....++|||+|||+.+      |+++|+++|..||.|..+.+       . ..++.++|||||+|.+.++|.+|+ .|||
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i-------~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g   83 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY-------P-EEDGKTKGYIFLEYASPAHAVDAVKNADG   83 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEEC-------C-CBTTBSCCEEEEEECSSSHHHHHHHHCSS
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEe-------e-CCCCCeeeEEEEEECCHHHHHHHHHHhCC
Confidence            3456899999999999      88999999999998644211       0 124467899999999999999999 5999


Q ss_pred             ceecCc-eEEEcCCCCCC
Q 013837          244 IIFEGV-AVRVRRPTDYN  260 (435)
Q Consensus       244 ~~~~g~-~l~v~~~~~~~  260 (435)
                      ..|.|+ +|.|.++.+..
T Consensus        84 ~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           84 YKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             EECSTTCEEEEECSCCCC
T ss_pred             cccCCCceEEEEEcchHh
Confidence            999998 99999987543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.51  E-value=2.8e-14  Score=112.36  Aligned_cols=74  Identities=20%  Similarity=0.369  Sum_probs=65.3

Q ss_pred             ccCCeEEEcCCCCC-CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          172 RHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ...++|||+|||+. +|+++|+++|..||.|.            .+.+  ++|||||+|.+.++|.+|+ .|++..|.|+
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~------------~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   90 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVA------------GCSV--HKGYAFVQYSNERHARAAVLGENGRVLAGQ   90 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCS------------EEEE--ETTEEEEECSSSHHHHHHHHHHTTCEETTE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeE------------EEEE--eCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            34689999999999 99999999999999753            3333  6899999999999999999 7999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        91 ~l~V~~a~~~  100 (110)
T 1wf1_A           91 TLDINMAGEP  100 (110)
T ss_dssp             ECCEEESCCC
T ss_pred             EEEEEECCCC
Confidence            9999988643

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=2.8e-14  Score=105.43  Aligned_cols=71  Identities=13%  Similarity=0.150  Sum_probs=61.1

Q ss_pred             CCe-EEEcCCCCCCCHHH----HHHHHHHHH-HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          174 ARR-VYVGGLPPLANEQA----IATFFSQVM-TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       174 ~~~-l~V~nlp~~~t~~~----l~~~f~~~G-~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      +.| |||+|||+.+++++    |+++|.+|| +|+            ++ +   .|+|||+|.+.++|..|+ .|+|..|
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl------------~V-t---gG~AfV~F~~~esA~~A~~~l~G~~l   71 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVL------------SI-T---GCSAILRFINQDSAERAQKRMENEDV   71 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEE------------EC-C---TTCEEEEESSHHHHHHHHHHHTTCCS
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeE------------EE-e---cCEEEEEECCHHHHHHHHHHhcCCcc
Confidence            445 99999999999988    558999995 854            33 2   299999999999999999 6999999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|++|.|.+++...
T Consensus        72 ~gr~i~v~~A~~~s   85 (96)
T 2diu_A           72 FGNRIIVSFTPKNR   85 (96)
T ss_dssp             SSSCCEEESSCCSC
T ss_pred             CCceEEEEecCCCc
Confidence            99999999987654

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=99.51  E-value=2.1e-14  Score=112.53  Aligned_cols=79  Identities=16%  Similarity=0.189  Sum_probs=65.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      ++.+ ..+.++|||||+|.+.++|.+|+ .|++..|.|+.
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   99 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAA------VHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLDGRP   99 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEC-TTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEEC-CCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            4578999999999999999999999999854311      0111 13456899999999999999999 59999999999


Q ss_pred             EEEcCCC
Q 013837          251 VRVRRPT  257 (435)
Q Consensus       251 l~v~~~~  257 (435)
                      |.|.++.
T Consensus       100 l~V~~a~  106 (107)
T 3ulh_A          100 MNIQLVT  106 (107)
T ss_dssp             CEEEEEC
T ss_pred             EEEEEeC
Confidence            9998764

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.51  E-value=2.5e-14  Score=112.68  Aligned_cols=83  Identities=20%  Similarity=0.167  Sum_probs=66.7

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|+|..|.|+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~   96 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHL------NLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   96 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEC------CBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            346789999999999999999999999997433110      011112445799999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        97 ~l~V~~a~~~  106 (110)
T 1oo0_B           97 TIQVDWCFVK  106 (110)
T ss_dssp             ECEEEESEES
T ss_pred             EEEEEEcccC
Confidence            9999987543

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.51  E-value=2.3e-14  Score=110.07  Aligned_cols=77  Identities=19%  Similarity=0.360  Sum_probs=67.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHH----HHHHHHHHhhcCCCCCCCCceEEEE---ecCCCcEEEEEecCHHHHHHHH-HhCC
Q 013837          172 RHARRVYVGGLPPLANEQAIA----TFFSQVMTAIGGNSAGPGDAVVNVY---INHEKKFAFVEMRTVEEASNAM-ALDG  243 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~----~~f~~~G~i~~~~~~~~~~~v~~~~---~~~~~g~afv~f~~~~~a~~a~-~l~~  243 (435)
                      .+.++|||+|||..+++++|+    ++|..||.|            ..+.   .+.++|||||+|.+.++|..|+ .|+|
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i------------~~v~i~~~~~~~g~afV~f~~~~~A~~A~~~l~g   73 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQI------------LDILVSRSLKMRGQAFVIFKEVSSATNALRSMQG   73 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCE------------EEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCE------------EEEEEEcCCCcCcEEEEEeCCHHHHHHHHHHhCC
Confidence            467899999999999999999    999999974            3443   3467899999999999999999 5999


Q ss_pred             ceecCceEEEcCCCCCC
Q 013837          244 IIFEGVAVRVRRPTDYN  260 (435)
Q Consensus       244 ~~~~g~~l~v~~~~~~~  260 (435)
                      ..|.|+.|.|.++....
T Consensus        74 ~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           74 FPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             CEETTEECEEEECSSCC
T ss_pred             CEECCcEEEEEEccCCC
Confidence            99999999999987654

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.51  E-value=4.7e-15  Score=120.58  Aligned_cols=81  Identities=19%  Similarity=0.192  Sum_probs=67.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      ....++|||+|||+.+|+++|+++|..||.   |..+.      ++.+ ..+.++|||||+|.+.++|.+||++|+..|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~------i~~d-~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~  113 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVH------FIYT-REGRQSGEAFVELGSEDDVKMALKKDRESMG  113 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEE------EEEC-SSSCEEEEEEEECSSHHHHHHHHTTTEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEE------EEEC-CCCCCCeEEEEEECCHHHHHHHHhcCCCEEC
Confidence            456789999999999999999999999998   43311      1122 2367789999999999999999999999999


Q ss_pred             CceEEEcCCCC
Q 013837          248 GVAVRVRRPTD  258 (435)
Q Consensus       248 g~~l~v~~~~~  258 (435)
                      |+.|.|.++..
T Consensus       114 gr~i~V~~a~~  124 (136)
T 2hgl_A          114 HRYIEVFKSHR  124 (136)
T ss_dssp             SSEEEEEECCH
T ss_pred             CEEEEEEECCh
Confidence            99999998653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=3.9e-14  Score=110.31  Aligned_cols=82  Identities=21%  Similarity=0.370  Sum_probs=67.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHH-HHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCce-ecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQ-VMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGII-FEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~-~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~-~~g  248 (435)
                      ...++|||+|||+.+|+++|+++|.. ||.|..+.      ++.+. ++.++|||||+|.+.++|.+|+ .|++.. |.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~------i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g   79 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGK------VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGS   79 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEE------EEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEE------EEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCC
Confidence            45689999999999999999999999 99864321      01111 4556899999999999999999 599999 999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        80 ~~l~v~~a~~~~   91 (104)
T 2dhg_A           80 KPVRLSVAIPKA   91 (104)
T ss_dssp             SCCCCCBCCCCC
T ss_pred             EeEEEEEccCCC
Confidence            999999986544

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=6e-14  Score=109.04  Aligned_cols=84  Identities=21%  Similarity=0.315  Sum_probs=67.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+||. ++..|.|+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~   83 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ------VKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGR   83 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTE
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEE------EEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCe
Confidence            345678999999999999999999999999864311      01111235568999999999999999997 57899999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        84 ~l~v~~a~~~~   94 (103)
T 2cqg_A           84 WCDCKLPNSKQ   94 (103)
T ss_dssp             EEEEECCCTTC
T ss_pred             EEEEEecCCCC
Confidence            99999987653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=9.6e-14  Score=110.37  Aligned_cols=84  Identities=18%  Similarity=0.277  Sum_probs=66.8

Q ss_pred             hhcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       169 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ......++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|| .+++ .|.
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~   84 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV------ITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IID   84 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEE------SCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EET
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEE------EEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCC
Confidence            34557799999999999999999999999998533110      111113456899999999999999999 4887 899


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |+.|.|.++...
T Consensus        85 g~~l~V~~a~~~   96 (116)
T 2cqd_A           85 GRKANVNLAYLG   96 (116)
T ss_dssp             TEECEEEESTTT
T ss_pred             CEEEEEEEcccC
Confidence            999999998654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.3e-14  Score=112.04  Aligned_cols=82  Identities=15%  Similarity=0.182  Sum_probs=66.7

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.       +.....+.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~-------i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRAD-------ILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR   84 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEE-------EEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE-------EEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCC
Confidence            34678999999999999999999999999854311       111112345799999999999999999 4999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        85 ~l~v~~a~~~   94 (114)
T 2do0_A           85 PMHVKMDERA   94 (114)
T ss_dssp             ECEEEECSCC
T ss_pred             EEEEEEcccC
Confidence            9999987654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=4.4e-14  Score=107.78  Aligned_cols=77  Identities=23%  Similarity=0.386  Sum_probs=64.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCc-EEEEEecCHHHHHHHHHhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g-~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|            ..+......+ ||||+|.+.++|.+|++|++..|.|+.
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v------------~~v~~~~~~g~~afV~f~~~~~a~~ai~l~g~~~~g~~   73 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPV------------ASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSLGGHR   73 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCE------------EEEEECSSSCCEEEEEESSHHHHHHHHTCSCCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCe------------EEEEEcCCCCcEEEEEECCHHHHHHHHhcCCeEECCEE
Confidence            356799999999999999999999999985            3333332222 999999999999999999999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        74 l~V~~a~~~~   83 (94)
T 2e5g_A           74 LRVRPREQKE   83 (94)
T ss_dssp             CCCBCSCCSC
T ss_pred             EEEEECCcCC
Confidence            9999876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=6.7e-15  Score=114.28  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=66.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..|+.+.         .+.+...+.++|||||+|.+.++|.+|| .||+..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~---------~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---------IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEE---------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEE---------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            35678999999999999999999999774321         1222234566899999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        83 ~l~V~~a~~~~   93 (102)
T 2fc8_A           83 KVTLDWAKPKG   93 (102)
T ss_dssp             ECEEEECCCCC
T ss_pred             EEEEEEecCCC
Confidence            99999987654

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=1e-13  Score=108.89  Aligned_cols=83  Identities=20%  Similarity=0.243  Sum_probs=65.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHH-hhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC--CceecC
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMT-AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD--GIIFEG  248 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~-i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~--~~~~~g  248 (435)
                      ..++|||+|||..+|+++|+++|..||. |..+.++     ..+..++.++|||||+|.+.++|..|+ .|+  +..|.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~-----~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g   81 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVY-----ASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG   81 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECC-----SSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEE-----ccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC
Confidence            5689999999999999999999999987 4331110     011112367899999999999999999 585  589999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus        82 ~~l~V~~a~~~~   93 (109)
T 2dis_A           82 HQIAVDWAEPEI   93 (109)
T ss_dssp             BCCEEEESCSSC
T ss_pred             CeEEEEEcCCCC
Confidence            999999987654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.50  E-value=2.3e-14  Score=115.82  Aligned_cols=84  Identities=21%  Similarity=0.190  Sum_probs=67.4

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||+.+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHL------NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------EecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            345789999999999999999999999997533111      111113445899999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus        93 ~l~v~~a~~~~  103 (126)
T 3ex7_B           93 PISVDWCFVRG  103 (126)
T ss_dssp             BCEEEESEESS
T ss_pred             EEEEEEecCCC
Confidence            99999886543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.50  E-value=2.2e-14  Score=106.25  Aligned_cols=72  Identities=19%  Similarity=0.256  Sum_probs=60.3

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          174 ARRVYVGGLPPLA------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       174 ~~~l~V~nlp~~~------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      +++|||+|||..+      |+++|+++|.+||.|..+.+        ...++.++|||||+|.+.++|.+|+ .|||..|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i--------~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~   72 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--------PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL   72 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEEC--------CCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEe--------cCCCCcEeEEEEEEECCHHHHHHHHHHhcCccc
Confidence            3689999999999      78999999999998544211        1124467899999999999999999 5999999


Q ss_pred             cCc-eEEE
Q 013837          247 EGV-AVRV  253 (435)
Q Consensus       247 ~g~-~l~v  253 (435)
                      .|+ +|.|
T Consensus        73 ~g~~~l~V   80 (81)
T 2krb_A           73 DKQHTFRV   80 (81)
T ss_dssp             SSSSCCCC
T ss_pred             CCceeEEe
Confidence            999 8877

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=2.6e-15  Score=116.33  Aligned_cols=79  Identities=27%  Similarity=0.191  Sum_probs=65.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..||. +.+.      ++.+ ..+.++|||||+|.+.++|.+||++|+..|.|+.|
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~------i~~d-~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i   84 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVH------IEIG-PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYV   84 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEE------EEES-SSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEE------EEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEE
Confidence            45689999999999999999999999983 2211      1122 24567899999999999999999999999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        85 ~V~~~~~   91 (102)
T 1wez_A           85 ELFLNST   91 (102)
T ss_dssp             EEEEECC
T ss_pred             EEEECCC
Confidence            9987653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.50  E-value=6e-15  Score=120.49  Aligned_cols=84  Identities=20%  Similarity=0.285  Sum_probs=69.5

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..|.|+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i------~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~  117 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI------PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR  117 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEEC------CCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEE------EecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            456789999999999999999999999998644211      111224567899999999999999999 5999999999


Q ss_pred             eEEEcCCCCCC
Q 013837          250 AVRVRRPTDYN  260 (435)
Q Consensus       250 ~l~v~~~~~~~  260 (435)
                      .|.|.++....
T Consensus       118 ~l~V~~a~~~~  128 (135)
T 2lea_A          118 ELRVQMARYGR  128 (135)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999987543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.50  E-value=5e-14  Score=113.47  Aligned_cols=82  Identities=16%  Similarity=0.148  Sum_probs=68.1

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCc
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGV  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~  249 (435)
                      ....++|||+|||..+++++|+++|..||.|..+.       +.....+.++|||||+|.+.++|.+|+. ||+..|.|+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~-------i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~  104 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA-------VDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR  104 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEE-------EECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEE-------EEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCc
Confidence            35678999999999999999999999999864421       1111145678999999999999999995 999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus       105 ~l~V~~a~~~  114 (124)
T 2kt5_A          105 PMDIQLVASQ  114 (124)
T ss_dssp             EEEEEEECCT
T ss_pred             EEEEEEeCCC
Confidence            9999987654

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.49  E-value=1.5e-14  Score=108.94  Aligned_cols=73  Identities=23%  Similarity=0.334  Sum_probs=63.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+.+++++|+++|.+| .|..            +.+..++|||||+|.+.++|.+|+ .|||..+.|++|
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~------------~~i~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   70 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKY------------CYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCC------------EEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEE------------EEEeCCCcEEEEEECCHHHHHHHHHHhCCCeECCcEE
Confidence            46799999999999999999999999 6432            333378999999999999999999 599999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        71 ~V~~a~~   77 (88)
T 1wg1_A           71 IVQLQPT   77 (88)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998754

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.49  E-value=3.9e-14  Score=119.00  Aligned_cols=85  Identities=21%  Similarity=0.286  Sum_probs=68.4

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|| .||+..|.|
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  108 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKII------MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD  108 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            345678999999999999999999999999854310      0011112456799999999999999999 499999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.++....
T Consensus       109 ~~l~V~~a~~~~  120 (156)
T 1h2v_Z          109 RIIRTDWDAGFK  120 (156)
T ss_dssp             EECEEEEESCCC
T ss_pred             eEEEEEECCCCC
Confidence            999999987654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=1.1e-14  Score=116.35  Aligned_cols=83  Identities=24%  Similarity=0.260  Sum_probs=66.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE--EecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV--YINHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~--~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      ....++|||+|||+.+|+++|+++|..||.|.+.     ...|..+  ..+.++|||||+|.+.++|.+||+.++..|.|
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~-----v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~g   94 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGG-----KEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGK   94 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTG-----GGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCC-----cceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCC
Confidence            3567899999999999999999999999875210     0012222  35667899999999999999999779999999


Q ss_pred             ceEEEcCCCC
Q 013837          249 VAVRVRRPTD  258 (435)
Q Consensus       249 ~~l~v~~~~~  258 (435)
                      +.|.|..+..
T Consensus        95 R~i~V~~a~~  104 (123)
T 2dha_A           95 RYIELFRSTA  104 (123)
T ss_dssp             CEECCEEECH
T ss_pred             eEEEEEECCH
Confidence            9999987653

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.49  E-value=1.7e-14  Score=110.61  Aligned_cols=75  Identities=15%  Similarity=0.298  Sum_probs=64.4

Q ss_pred             cccCCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ..+.++|||+|||+ .+|+++|+++|..||.|.            .+.+  .+|||||+|.+.++|..|+ .|++..+.|
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~------------~v~i--~~g~afV~f~~~~~A~~A~~~l~g~~~~g   72 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM------------QINI--KNAFGFIQFDNPQSVRDAIECESQEMNFG   72 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCC------------EEEE--ETTEEEEEESCHHHHHHHHHHHTCSSCBT
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEE------------EEEE--eCCEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            35678999999998 999999999999999753            3333  3899999999999999999 599999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++...
T Consensus        73 ~~l~V~~a~~~   83 (96)
T 2kvi_A           73 KKLILEVSSSN   83 (96)
T ss_dssp             TTBCEEEEECC
T ss_pred             cEEEEEEcCcC
Confidence            99999987654

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.49  E-value=2.2e-14  Score=120.87  Aligned_cols=82  Identities=21%  Similarity=0.290  Sum_probs=68.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .|||..|.|++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i------~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~  141 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI------PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE  141 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEC------CCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEE------eecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            45789999999999999999999999998543211      111124567899999999999999999 59999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++...
T Consensus       142 l~v~~a~~~  150 (158)
T 2kn4_A          142 LRVQMARYG  150 (158)
T ss_dssp             EEEEEECCS
T ss_pred             EEEEECCCC
Confidence            999988754

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=2.3e-14  Score=112.99  Aligned_cols=77  Identities=19%  Similarity=0.288  Sum_probs=65.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHH---HHHHHHHHhhcCCCCCCCCceEEEEec---------CCCcEEEEEecCHHHHHHHH
Q 013837          172 RHARRVYVGGLPPLANEQAIA---TFFSQVMTAIGGNSAGPGDAVVNVYIN---------HEKKFAFVEMRTVEEASNAM  239 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~---~~f~~~G~i~~~~~~~~~~~v~~~~~~---------~~~g~afv~f~~~~~a~~a~  239 (435)
                      ...++|||+|||+.+++++|.   ++|.+||.|..            +.+.         .++|||||+|.+.++|.+|+
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~------------v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai   80 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHK------------VVINNSTSYAGSQGPSASAYVTYIRSEDALRAI   80 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEE------------EEEECCSSCCSSSCCCEEEEEEESSHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEE------------EEEecCCCcCccCCCCeEEEEEECcHHHHHHHH
Confidence            356799999999999999999   99999998543            3322         34589999999999999999


Q ss_pred             -HhCCceecCceEEEcCCCCCC
Q 013837          240 -ALDGIIFEGVAVRVRRPTDYN  260 (435)
Q Consensus       240 -~l~~~~~~g~~l~v~~~~~~~  260 (435)
                       .||+..|.|++|.|.++....
T Consensus        81 ~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           81 QCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             HHHTTEEETTEEEEEESCCCCS
T ss_pred             HHhCCCEECCEEEEEEeccccc
Confidence             599999999999999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=2.7e-14  Score=111.49  Aligned_cols=78  Identities=17%  Similarity=0.218  Sum_probs=63.7

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ...+|||+|||+.+|+++|+++|..| .|..+.      ++.+ ..+.++|||||+|.+.++|.+||.+|+..|+|+.|.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~------i~~d-~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   86 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVH------LLKD-HVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVE   86 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEE------ECCC-TTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEE------EEEC-CCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEE
Confidence            45799999999999999999999999 542211      0111 125678999999999999999999999999999999


Q ss_pred             EcCCCC
Q 013837          253 VRRPTD  258 (435)
Q Consensus       253 v~~~~~  258 (435)
                      |..+..
T Consensus        87 V~~a~~   92 (109)
T 2dnn_A           87 VSPATE   92 (109)
T ss_dssp             EEECCH
T ss_pred             EEECCc
Confidence            987653

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.49  E-value=4.2e-15  Score=116.39  Aligned_cols=81  Identities=17%  Similarity=0.207  Sum_probs=67.5

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHH---hhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMT---AIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~---i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~  247 (435)
                      ....++|||+|||+.+|+++|+++|..||.   |..+.      ++.+.. +.++|||||+|.+.++|.+||.+++..|+
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~------i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~   80 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIH------FLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMG   80 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEE------CCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEE------EEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeC
Confidence            356789999999999999999999999887   43321      122222 67899999999999999999999999999


Q ss_pred             CceEEEcCCCC
Q 013837          248 GVAVRVRRPTD  258 (435)
Q Consensus       248 g~~l~v~~~~~  258 (435)
                      |+.|.|.++..
T Consensus        81 gr~i~V~~a~~   91 (107)
T 2lmi_A           81 QRYVEVYEINN   91 (107)
T ss_dssp             SSCCCCEECCH
T ss_pred             CeEEEEEECCH
Confidence            99999988754

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.49  E-value=3.1e-14  Score=124.64  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=72.1

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||+|||. .+|+++|+++|+.||.|..|.|+.++     +|||||+|.+.++|.+|+..|||..|.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            46899999999 99999999999999999999998874     7899999999999999999999999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ...
T Consensus        78 ~~~   80 (198)
T 1qm9_A           78 HQN   80 (198)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.49  E-value=8.3e-14  Score=116.14  Aligned_cols=78  Identities=28%  Similarity=0.412  Sum_probs=68.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC-CCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH-EKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~-~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      .....++|||+|||+.+|+++|+++|..||.            |..+.+.. ++|||||+|.+.++|..|+ .|||..|.
T Consensus        69 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~------------i~~v~i~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~  136 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGP------------LRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLC  136 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSCHHHHHHHHHHSC------------EEEEEECSSSCSEEEEEESSHHHHHHHHHHHSSSCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhCC------------EEEEEEeeCCCcEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            3456789999999999999999999999997            55565554 4999999999999999999 59999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |++|.|.++.+.
T Consensus       137 g~~l~v~~a~~~  148 (150)
T 2i2y_A          137 GCRVRVELSNGE  148 (150)
T ss_dssp             SSCCEEEECCCC
T ss_pred             CeEEEEEEcCCC
Confidence            999999987643

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.49  E-value=1.2e-13  Score=108.45  Aligned_cols=76  Identities=14%  Similarity=0.087  Sum_probs=66.3

Q ss_pred             CCCCeEEEcCCCCCC----------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee
Q 013837          292 EGPDRVFVGGLPYYF----------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~----------te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~  361 (435)
                      .++++|.|.||-...          .++||+++|++||.|+.|.|.++.    ++|||||+|.+.++|.+|+..|||.+|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            457799999994322          236899999999999999987653    489999999999999999999999999


Q ss_pred             CCeEEEEEEc
Q 013837          362 GDKTLTVRRA  371 (435)
Q Consensus       362 ~g~~l~V~~a  371 (435)
                      +|+.|.|.|+
T Consensus        81 ~GR~i~v~~~   90 (114)
T 3s6e_A           81 AGKMITAAYV   90 (114)
T ss_dssp             TTEECEEEEE
T ss_pred             CCEEEEEEEE
Confidence            9999999998

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.48  E-value=1e-13  Score=114.16  Aligned_cols=81  Identities=22%  Similarity=0.349  Sum_probs=65.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .||+..|.|
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  132 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG  132 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEEC------CCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETT
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEE------eecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456789999999999999999999999998533110      111122456899999999999999999 699999999


Q ss_pred             ceEEEcCC
Q 013837          249 VAVRVRRP  256 (435)
Q Consensus       249 ~~l~v~~~  256 (435)
                      +.|.|.++
T Consensus       133 ~~l~v~~A  140 (140)
T 2ku7_A          133 RTIRVNLA  140 (140)
T ss_dssp             EEEEEEC-
T ss_pred             EEEEEEeC
Confidence            99999874

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=7.9e-14  Score=106.84  Aligned_cols=76  Identities=18%  Similarity=0.312  Sum_probs=65.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE---EecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV---YINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~---~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ...++|||+|||+.+|+++|+++|..||.            |..+   ......+.|||+|.+.++|..|+ .|||..|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~------------v~~~~~i~~~~~~~~afV~f~~~~~a~~Ai~~l~g~~~~   80 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGV------------VESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQLE   80 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSC------------EEEEEEECCSSSSEEEEEEESSHHHHHHHHHHHTTCBCS
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCC------------eEEEEEeecCCCCCEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            35689999999999999999999999997            4444   22334566999999999999999 59999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |++|.|.++.+.
T Consensus        81 g~~l~V~~a~~~   92 (96)
T 2e44_A           81 NFTLKVAYIPDE   92 (96)
T ss_dssp             SCBCEEEECCCC
T ss_pred             CcEEEEEEcCcc
Confidence            999999988754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=4.2e-15  Score=109.00  Aligned_cols=75  Identities=12%  Similarity=0.250  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~l~v  253 (435)
                      ++|||+|||..+++++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|++ ++ ..+.|++|.|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~------i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v   73 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECL------VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDP   73 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEE------EECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEE
Confidence            4799999999999999999999999864311      11111245678999999999999999995 66 9999999999


Q ss_pred             cCC
Q 013837          254 RRP  256 (435)
Q Consensus       254 ~~~  256 (435)
                      .++
T Consensus        74 ~~a   76 (77)
T 1uaw_A           74 KVA   76 (77)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            875

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=1.3e-14  Score=108.58  Aligned_cols=79  Identities=19%  Similarity=0.333  Sum_probs=64.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+.+++++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~------i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~   77 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTK------AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   77 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEE------EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEE
Confidence            568999999999999999999999999854311      0111123456899999999999999999 599999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      +|.++.
T Consensus        78 ~~~~~~   83 (85)
T 1x4e_A           78 KQSGPS   83 (85)
T ss_dssp             CSSCCC
T ss_pred             eecCCC
Confidence            998754

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.47  E-value=1.1e-13  Score=126.57  Aligned_cols=78  Identities=32%  Similarity=0.538  Sum_probs=71.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|.++      +|||||+|.+.++|.+|+..|||..|.|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            44578999999999999999999999999999998653      789999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .+..
T Consensus        94 ~~~~   97 (261)
T 3sde_A           94 THGA   97 (261)
T ss_dssp             CCSS
T ss_pred             ccCC
Confidence            7643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.47  E-value=4.1e-13  Score=117.37  Aligned_cols=75  Identities=21%  Similarity=0.491  Sum_probs=66.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~----G-------~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      .++|||+|||..+|+++|+++|+.|    |       .|..+.+      +.++|||||+|.+.++|.+|| .|||..|.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            5799999999999999999999999    5       4555554      345899999999999999999 79999999


Q ss_pred             CeEEEEEEccCCC
Q 013837          363 DKTLTVRRATASS  375 (435)
Q Consensus       363 g~~l~V~~a~~~~  375 (435)
                      |+.|.|.++....
T Consensus        77 g~~i~v~~~~~~~   89 (198)
T 2yh0_A           77 GQSLKIRRPHDYQ   89 (198)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CceEEEeCCCCCC
Confidence            9999999997654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.20  E-value=3.9e-15  Score=118.47  Aligned_cols=90  Identities=20%  Similarity=0.234  Sum_probs=71.3

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCC--CCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGP--GDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~--~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ..+.++|||+|||..+++++|+++|..||.|..+.....  ..++.+..++.++|||||+|.+.++|.+|+ .||+..|.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            346789999999999999999999999999754110000  012333455678999999999999999999 59999999


Q ss_pred             CceEEEcCCCCCC
Q 013837          248 GVAVRVRRPTDYN  260 (435)
Q Consensus       248 g~~l~v~~~~~~~  260 (435)
                      |+.|.|.++....
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999986543

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=4.2e-13  Score=102.69  Aligned_cols=76  Identities=12%  Similarity=0.182  Sum_probs=63.7

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          294 PDRVFVGGLP-------YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       294 ~~~l~V~nLp-------~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ...|.|.-..       ..+|+++|+++|++||.|..|.|+     +.++|||||+|.+.++|..||..+++  +.|+.|
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l   82 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPL   82 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBC
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeE
Confidence            3466665543       458999999999999999999987     35799999999999999999997554  679999


Q ss_pred             EEEEccCCCC
Q 013837          367 TVRRATASSG  376 (435)
Q Consensus       367 ~V~~a~~~~~  376 (435)
                      +|.|+..+..
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999987653

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.46  E-value=1.7e-14  Score=109.15  Aligned_cols=79  Identities=29%  Similarity=0.415  Sum_probs=62.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      ++|||+|||..+++++|+++|..||.|..+.+      +.+..++.++|||||+|.+.+ |..|+ .|||..+.|+.|.|
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i------~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V   74 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKL------IYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRV   74 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEE------CCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSE
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEE------EEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEE
Confidence            58999999999999999999999998643110      111123567899999999999 99999 59999999999999


Q ss_pred             cCCCCCC
Q 013837          254 RRPTDYN  260 (435)
Q Consensus       254 ~~~~~~~  260 (435)
                      .++....
T Consensus        75 ~~a~~~~   81 (90)
T 2ki2_A           75 TEANPKK   81 (90)
T ss_dssp             EEC----
T ss_pred             EEcCCCC
Confidence            9886543

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.46  E-value=5.8e-14  Score=111.35  Aligned_cols=73  Identities=26%  Similarity=0.361  Sum_probs=61.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.            |..+.+... |||||+|.+.++|.+|| .||+..|.|+.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~------------v~~~~i~~~-g~afV~f~~~~~a~~Ai~~l~g~~~~gr~   80 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNTKFRSHE   80 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEECTT-SEEEEEESSHHHHHHHHHHHTTCBCCCTT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCC------------eEEEEEecC-CEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            35689999999999999999999999997            556666555 99999999999999999 59999999998


Q ss_pred             -----EEEcCCC
Q 013837          251 -----VRVRRPT  257 (435)
Q Consensus       251 -----l~v~~~~  257 (435)
                           |.|....
T Consensus        81 ~~~~~i~v~~~~   92 (115)
T 3beg_B           81 GETAYIRVKVDG   92 (115)
T ss_dssp             SCCCBCEEEECC
T ss_pred             eeeEEEEeccCC
Confidence                 5555443

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.46  E-value=1.8e-13  Score=113.59  Aligned_cols=77  Identities=17%  Similarity=0.194  Sum_probs=64.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      ...+|||+||++.+|+++|+++|++||.|..         |. +.....+|||||+|.+.++|..|+ .|||..|.|  +
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~---------V~-i~~k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~  114 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLK---------II-TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC  114 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEE---------EE-EEESSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEE---------EE-EEeCCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCc
Confidence            3457999999999999999999999998643         21 223446789999999999999999 699999966  9


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|+|.|+...
T Consensus       115 ~L~V~~Ak~~  124 (164)
T 1sjr_A          115 TLRIDFSKLT  124 (164)
T ss_dssp             CEEEEECSSS
T ss_pred             EEEEEEecCC
Confidence            9999998754

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=4e-14  Score=112.24  Aligned_cols=81  Identities=12%  Similarity=0.266  Sum_probs=65.3

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee--
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~--  246 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+.      ++.+ ..+.++|||||+|.+.++|.+|+ .|||..|  
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~------i~~~-~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~   93 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR------ILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT   93 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE------EEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEE------EEEC-CCCCcceEEEEEECCHHHHHHHHHHhCCCEEcC
Confidence            345678999999999999999999999999864321      0111 13556899999999999999999 5999999  


Q ss_pred             ------cCceEEEcCCC
Q 013837          247 ------EGVAVRVRRPT  257 (435)
Q Consensus       247 ------~g~~l~v~~~~  257 (435)
                            .+++|.|.++.
T Consensus        94 ~~~~~~~~~~l~v~~a~  110 (114)
T 1x5o_A           94 PPGVSAPTEPLLCKFSG  110 (114)
T ss_dssp             CTTSCCCSSCBEEEECC
T ss_pred             CccccCCCCceeEEccC
Confidence                  57788888775

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.45  E-value=6.2e-15  Score=120.26  Aligned_cols=82  Identities=24%  Similarity=0.184  Sum_probs=66.2

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCc
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGV  249 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~  249 (435)
                      .....++|||+|||+++|+++|+++|..|| ++.+.+      +.+. .+.++|||||+|.+.++|.+||++|+..|.|+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i------~~d~-~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR  113 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHI------EIGP-DGRVTGEADVEFATHEEAVAAMSKDRANMQHR  113 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEEC------CCSS-SSCSSCCCEEECSHHHHHHHHTTCCSCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEE------EECC-CCCCceEEEEEeCCHHHHHHHHhhCCCEECCE
Confidence            345678999999999999999999999998 533211      2221 26789999999999999999999999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus       114 ~i~V~~a~~~  123 (139)
T 2hgn_A          114 YIELFLNSTT  123 (139)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999876543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.44  E-value=1.2e-14  Score=116.26  Aligned_cols=75  Identities=20%  Similarity=0.224  Sum_probs=62.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEecCHHHHHHHHHhCCcee
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAMALDGIIF  246 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-----~~~~g~afv~f~~~~~a~~a~~l~~~~~  246 (435)
                      ...++|||+|||+.+|+++|+++|..| .|+.          ..+.+     +.++|||||+|.+.++|.+||++++..|
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~----------~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l  108 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVP----------NGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERI  108 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEE----------EEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCB
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-Ccee----------eEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEE
Confidence            456889999999999999999999999 4320          03332     5678999999999999999998888999


Q ss_pred             cCceEEEcCCC
Q 013837          247 EGVAVRVRRPT  257 (435)
Q Consensus       247 ~g~~l~v~~~~  257 (435)
                      .|+.|.|.++.
T Consensus       109 ~gR~I~V~~a~  119 (126)
T 2hgm_A          109 GHRYIEVFKSS  119 (126)
T ss_dssp             TTBCCCCEEEC
T ss_pred             CCEEEEEEECC
Confidence            99999998653

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.44  E-value=1.6e-14  Score=128.91  Aligned_cols=80  Identities=15%  Similarity=0.144  Sum_probs=65.4

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHH--HhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVM--TAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G--~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ..++|||+|||+.+|+++|+++|..||  .|+.+.      ++.+..++.++|||||+|.+.++|.+|| .||+..|.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~------i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr  140 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIK------FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ  140 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEE------EEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTB
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEE------EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCE
Confidence            567999999999999999999999999  754311      1111124567899999999999999999 5999999999


Q ss_pred             eEEEcCCCC
Q 013837          250 AVRVRRPTD  258 (435)
Q Consensus       250 ~l~v~~~~~  258 (435)
                      .|.|.++..
T Consensus       141 ~l~V~~a~~  149 (229)
T 3q2s_C          141 NPVVTPVNK  149 (229)
T ss_dssp             CCEEEECCH
T ss_pred             EeEEEECCC
Confidence            999998764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.43  E-value=1.9e-13  Score=109.14  Aligned_cols=75  Identities=19%  Similarity=0.243  Sum_probs=63.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcE-EEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~-afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      -..|||+||++.+|+++|+++|++||.|..         |...  ...+|| |||+|.+.++|..|+ .|||..|.|  +
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~yG~V~~---------V~i~--~~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~   96 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKFGTVLK---------IITF--TKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC   96 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTSSCEEE---------EEEE--EETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCcCCEEE---------EEEE--cCCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCc
Confidence            346889999999999999999999998643         2211  235687 999999999999999 699999998  9


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|+|.|++..
T Consensus        97 ~LrI~~ak~~  106 (130)
T 3zzy_A           97 TLRIDFSKLT  106 (130)
T ss_dssp             EEEEEECSCS
T ss_pred             EEEEEecCCC
Confidence            9999998754

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.43  E-value=2.6e-13  Score=107.94  Aligned_cols=73  Identities=16%  Similarity=0.102  Sum_probs=60.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcE-EEEEecCHHHHHHHH-HhCCceecC--ce
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKF-AFVEMRTVEEASNAM-ALDGIIFEG--VA  250 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~-afv~f~~~~~a~~a~-~l~~~~~~g--~~  250 (435)
                      ..|||+||++.+|+++|+++|++||.|..            +.+....|| |||+|.+.++|..|+ .|||..|.|  +.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~------------v~i~~~~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~   93 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQR------------IVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYAGCCT   93 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEE------------EEEEESSSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSE
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEE------------EEEEeCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCeE
Confidence            35789999999999999999999998643            222112486 999999999999999 699999987  69


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++...
T Consensus        94 l~V~~Ak~~  102 (124)
T 2e5i_A           94 LKIEYARPT  102 (124)
T ss_dssp             EEEECCSCS
T ss_pred             EEEEEecCC
Confidence            999988754

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.43  E-value=1.3e-13  Score=116.75  Aligned_cols=83  Identities=20%  Similarity=0.166  Sum_probs=66.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|.++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|| .|||..|.|+.
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~------i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~  143 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT  143 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEE------EEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4567999999999999999999999999854310      0011113445799999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus       144 l~V~~a~~~~  153 (165)
T 1rk8_A          144 IQVDWCFVKG  153 (165)
T ss_dssp             CEEEESEECC
T ss_pred             EEEEEecCCC
Confidence            9999876543

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.43  E-value=4.1e-13  Score=114.54  Aligned_cols=75  Identities=21%  Similarity=0.483  Sum_probs=66.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhc----C-------CeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESF----G-------TLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~----G-------~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      .++|||+|||..+|+++|+++|++|    |       .|..+.+..      ++|||||+|.+.++|.+|+ .|||..|.
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            4689999999999999999999999    6       666666643      4799999999999999999 79999999


Q ss_pred             CeEEEEEEccCCC
Q 013837          363 DKTLTVRRATASS  375 (435)
Q Consensus       363 g~~l~V~~a~~~~  375 (435)
                      |+.|.|.++....
T Consensus        77 g~~i~v~~~~~~~   89 (172)
T 2g4b_A           77 GQSLKIRRPHDYQ   89 (172)
T ss_dssp             TEECEEECCSSCC
T ss_pred             CceeeecCCcccC
Confidence            9999999987653

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.43  E-value=1.3e-13  Score=134.52  Aligned_cols=83  Identities=16%  Similarity=0.148  Sum_probs=70.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|.++|..||.|+.+.      ++.+..++.++|||||+|.+.++|.+|| .|||..|.|+.
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~------i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~  173 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIH------MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR  173 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEE------eeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEE
Confidence            3457999999999999999999999999875532      1233345678999999999999999999 69999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus       174 i~V~~a~~~~  183 (437)
T 3pgw_S          174 VLVDVERGRT  183 (437)
T ss_pred             EEEEEeCCCC
Confidence            9999987543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.42  E-value=2.6e-13  Score=102.15  Aligned_cols=75  Identities=28%  Similarity=0.450  Sum_probs=57.7

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHHHhCCc--ee
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGI--IF  246 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~~l~~~--~~  246 (435)
                      ......+|||+|||+++|+++|+++|++||.            |..+.+. .++|||||+|.+.++|.+   +++.  .+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~------------i~~v~i~~~srGfaFV~F~~~~~A~~---~~~~~~~~   71 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGE------------VVDVFIPKPFRAFAFVTFADDKVAQS---LCGEDLII   71 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSC------------EEEEECCSSCCSEEEEEESCHHHHHH---HTTCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCC------------EEEEEEeeCCCCEEEEEECCHHHHHH---HcCCCccc
Confidence            3456789999999999999999999999997            4444443 379999999999999984   3444  45


Q ss_pred             cCceEEEcCCCCC
Q 013837          247 EGVAVRVRRPTDY  259 (435)
Q Consensus       247 ~g~~l~v~~~~~~  259 (435)
                      .|+.|.|.++.+.
T Consensus        72 ~g~~v~v~~a~~k   84 (89)
T 3d2w_A           72 KGISVHISNAEPK   84 (89)
T ss_dssp             TTEEEEEEECC--
T ss_pred             CCEEEEEEEcCCC
Confidence            6999999987654

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.40  E-value=5.3e-13  Score=124.83  Aligned_cols=76  Identities=21%  Similarity=0.292  Sum_probs=66.1

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC---Ce-
Q 013837          291 AEGPDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG---DK-  364 (435)
Q Consensus       291 ~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~---g~-  364 (435)
                      ..++.+|||+|  |++.+|+++|+++|++||.|..|.|..      ++|||||+|.+.++|++||++|||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            46678999999  578999999999999999999887653      4799999999999999999999999883   44 


Q ss_pred             -EEEEEEcc
Q 013837          365 -TLTVRRAT  372 (435)
Q Consensus       365 -~l~V~~a~  372 (435)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             68888884

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.38  E-value=9.5e-14  Score=107.69  Aligned_cols=80  Identities=18%  Similarity=0.309  Sum_probs=65.5

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA  250 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~  250 (435)
                      ....++|||+|||..+|+++|+++|..||.|..+.      .+.+ ..+.++|||||+|.+.++|.+|+. ++..|+|+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~------i~~~-~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~   77 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVK------IITD-RTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKK   77 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEE------EEEC-TTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEE------EEEC-CCCCccceEEEEECCHHHHHHHHh-CCCeECCEE
Confidence            44668999999999999999999999999864311      0111 134568999999999999999999 999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.++..
T Consensus        78 l~v~~a~~   85 (102)
T 2xs2_A           78 LKLGPAIR   85 (102)
T ss_dssp             CEEEEEEE
T ss_pred             EEEEECCc
Confidence            99987653

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=3.4e-13  Score=101.47  Aligned_cols=75  Identities=24%  Similarity=0.375  Sum_probs=61.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ..++|||+|||..+|+++|+++|..||.|            ..+.+. .++|||||+|.+.++|.+|+.. ...+.|+.|
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i------------~~v~i~~~~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l   70 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDV------------MDVFIPKPFRAFAFVTFADDQIAQSLCGE-DLIIKGISV   70 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCC------------CEEECCSSCCSCCEEECSCHHHHHHTTTC-EEEETTEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCe------------eEEEEecCCCCEEEEEECCHHHHHHHhcC-CceeCCEEE
Confidence            56899999999999999999999999975            333332 3689999999999999865432 456689999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++....
T Consensus        71 ~v~~a~~~~   79 (88)
T 1wf0_A           71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEecCCCC
Confidence            999876543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.37  E-value=4.8e-13  Score=118.64  Aligned_cols=78  Identities=22%  Similarity=0.333  Sum_probs=68.4

Q ss_pred             cccCCeEEEcCCCCCC---------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-H
Q 013837          171 TRHARRVYVGGLPPLA---------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-A  240 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~---------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~  240 (435)
                      ....++|||+||+..+         ++++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~------------I~~v~v~~~kG~AFV~F~~~~~Ae~A~~a  198 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGD------------IDRIRYVESKNCGFVKFKYQANAEFAKEA  198 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSC------------EEEEEEEGGGTEEEEEESSHHHHHHHHHH
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCC------------EEEEEEECCCCEEEEEeCCHHHHHHHHHH
Confidence            4567899999999998         79999999999997            666666678999999999999999999 6


Q ss_pred             hCCcee------------cCceEEEcCCCCCC
Q 013837          241 LDGIIF------------EGVAVRVRRPTDYN  260 (435)
Q Consensus       241 l~~~~~------------~g~~l~v~~~~~~~  260 (435)
                      |+|..|            .|+.|.|.|+.+..
T Consensus       199 m~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~p  230 (240)
T 3u1l_A          199 MSNQTLLLPSDKEWDDRREGTGLLVKWANEDP  230 (240)
T ss_dssp             HTTCCCCCTTSTTGGGGGGSCCCEEEECC---
T ss_pred             hCCCEEeccccccccccCCCCEEEEEEccCCC
Confidence            999999            89999999987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.32  E-value=2.9e-13  Score=105.94  Aligned_cols=77  Identities=12%  Similarity=0.081  Sum_probs=63.1

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecC----HHH----HHHHHH--
Q 013837          175 RRVYVGGL----PPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT----VEE----ASNAMA--  240 (435)
Q Consensus       175 ~~l~V~nl----p~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~----~~~----a~~a~~--  240 (435)
                      .+|||+||    |+.+++.+|+++|..||+|..+.      .+.+..++.++|||||+|.+    +++    |.+|+.  
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~------li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~   76 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFE------AFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKH   76 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEE------EEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEE------EEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHh
Confidence            68999999    99999999999999999986642      35555677889999999996    433    777764  


Q ss_pred             -hCCceecCceEEEcCCC
Q 013837          241 -LDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       241 -l~~~~~~g~~l~v~~~~  257 (435)
                       ++|..|.|++|.|..-.
T Consensus        77 ~lng~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           77 ESSGCFIMGFKFEVILNK   94 (136)
T ss_dssp             TTTCEEETTEEEEEEECC
T ss_pred             hhcCCeecCcEEEEEECc
Confidence             79999999999998643

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A

Probab=99.31  E-value=2.1e-12  Score=112.04  Aligned_cols=81  Identities=19%  Similarity=0.240  Sum_probs=66.9

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE--ecCCCcEEEEEecCHHHHHHHHHhCCceecC
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY--INHEKKFAFVEMRTVEEASNAMALDGIIFEG  248 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~--~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g  248 (435)
                      ....++|||+|||+.+|+++|.++|..||.|..         |....  .+.++|||||+|.+.++|.+|++..+..|.|
T Consensus       106 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~---------v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~G  176 (193)
T 2voo_A          106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLN---------IQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKE  176 (193)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEE---------EEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETT
T ss_pred             ccccCEEEecCCCCcCCHHHHHHHHhcCCCEEE---------EEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECC
Confidence            345689999999999999999999999998543         21111  2456899999999999999999866779999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      +.|.|.+..++.
T Consensus       177 r~l~V~~~~~y~  188 (193)
T 2voo_A          177 TDLLILFKDDYF  188 (193)
T ss_dssp             EECEEEETTTC-
T ss_pred             EEEEEEEhHHHH
Confidence            999999887764

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=3.2e-12  Score=101.09  Aligned_cols=76  Identities=21%  Similarity=0.247  Sum_probs=57.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~---~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ...++|||+|||+.+|+++|+++|.+||.|. +.+      +.+..+   +.++|||||+|.+.++|.+|| .++  .++
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~------~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~   76 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDW------PHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EED   76 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EEC------TTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EET
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEE------eecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcC
Confidence            4578999999999999999999999999863 111      111112   567999999999999999999 462  356


Q ss_pred             CceEEEcCC
Q 013837          248 GVAVRVRRP  256 (435)
Q Consensus       248 g~~l~v~~~  256 (435)
                      |+.|.+...
T Consensus        77 G~~~~~~~~   85 (114)
T 2dnl_A           77 GKLYLCVSS   85 (114)
T ss_dssp             TEEEEEECC
T ss_pred             CcEEEeccC
Confidence            666665543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.25  E-value=1.2e-11  Score=95.83  Aligned_cols=77  Identities=19%  Similarity=0.109  Sum_probs=62.6

Q ss_pred             ccCCeEEEcCCCC-----CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE----ecCCCcEEEEEecCHHHHHHHH-Hh
Q 013837          172 RHARRVYVGGLPP-----LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY----INHEKKFAFVEMRTVEEASNAM-AL  241 (435)
Q Consensus       172 ~~~~~l~V~nlp~-----~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~----~~~~~g~afv~f~~~~~a~~a~-~l  241 (435)
                      .++++|+|.||..     .-++++|+++|++||.|..         +..+.    .+.++|||||+|.+.++|.+|+ .|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~---------v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~l   76 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGK---------CVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDL   76 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEE---------EEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEE---------EEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHH
Confidence            4578999999963     2378999999999998654         21121    1357899999999999999999 69


Q ss_pred             CCceecCceEEEcCCC
Q 013837          242 DGIIFEGVAVRVRRPT  257 (435)
Q Consensus       242 ~~~~~~g~~l~v~~~~  257 (435)
                      ||..|.|+.|.|.++.
T Consensus        77 nG~~~~Gr~i~v~~a~   92 (105)
T 2pe8_A           77 NGRYFGGRVVKACFYN   92 (105)
T ss_dssp             TTCEETTEECEEEECC
T ss_pred             CCCEECCcEEEEEEcC
Confidence            9999999999999875

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.23  E-value=1.4e-11  Score=97.08  Aligned_cols=78  Identities=22%  Similarity=0.245  Sum_probs=63.7

Q ss_pred             ccCCeEEEcCCCCCCC-----------HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-
Q 013837          172 RHARRVYVGGLPPLAN-----------EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-  239 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t-----------~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-  239 (435)
                      ...++|+|.||....+           +++|+++|.+||.|..         + .+....++|||||+|.+.++|.+|+ 
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~---------v-~i~~~~~~G~afV~f~~~~~A~~Ai~   82 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRK---------L-LLFDRHPDGVASVSFRDPEEADYCIQ   82 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSE---------E-EEETTCTTCEEEEECSCHHHHHHHHH
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeE---------E-EEecCCCCEEEEEEECCHHHHHHHHH
Confidence            4678999999944332           6899999999998644         2 2233347899999999999999999 


Q ss_pred             HhCCceecCceEEEcCCCCC
Q 013837          240 ALDGIIFEGVAVRVRRPTDY  259 (435)
Q Consensus       240 ~l~~~~~~g~~l~v~~~~~~  259 (435)
                      .|||..|.|++|.|.++.+.
T Consensus        83 ~lng~~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           83 TLDGRWFGGRQITAQAWDGT  102 (112)
T ss_dssp             HSTTCEETTEECEEEECCSC
T ss_pred             HcCCCEECCcEEEEEEeCCC
Confidence            69999999999999987653

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.19  E-value=6.5e-11  Score=86.69  Aligned_cols=72  Identities=19%  Similarity=0.290  Sum_probs=60.8

Q ss_pred             CCeEEEcCCCC----CCCH----HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeE
Q 013837          294 PDRVFVGGLPY----YFTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKT  365 (435)
Q Consensus       294 ~~~l~V~nLp~----~~te----~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~  365 (435)
                      ..||+|...+.    +.-.    .+|.+.|.+||.|..++|+.+.        +||+|.+.++|.+||+ |||..++|+.
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr~   77 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNRT   77 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTEE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCeE
Confidence            34777776652    2333    6789999999999999998873        8999999999999999 9999999999


Q ss_pred             EEEEEccCC
Q 013837          366 LTVRRATAS  374 (435)
Q Consensus       366 l~V~~a~~~  374 (435)
                      |+|+++++.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999999754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=7.5e-11  Score=92.44  Aligned_cols=75  Identities=13%  Similarity=0.127  Sum_probs=67.7

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcC-HHHHHHHHHHhC--CceeCCeEE
Q 013837          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD-PAVTDIACAALN--GLKMGDKTL  366 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~-~~~A~~Al~~l~--g~~~~g~~l  366 (435)
                      ....+.|+|+||+.. +++++|+++|+.||.|..|.+..+..      .|||+|.+ ..+|..|+..||  |..|+|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            455678999999999 99999999999999999999988754      59999999 899999999994  889999999


Q ss_pred             EEEEc
Q 013837          367 TVRRA  371 (435)
Q Consensus       367 ~V~~a  371 (435)
                      ++...
T Consensus        89 ~~evL   93 (121)
T 1owx_A           89 TWEVL   93 (121)
T ss_dssp             EEEEC
T ss_pred             EEEEC
Confidence            99876

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=99.15  E-value=5.3e-11  Score=111.32  Aligned_cols=75  Identities=17%  Similarity=0.235  Sum_probs=63.6

Q ss_pred             cccCCeEEEcC--CCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          171 TRHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       171 ~~~~~~l~V~n--lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ..+.++|||+|  |++.+|+++|+++|.+||.            |..+.+..++|||||+|.+.++|.+|+ .|||..+.
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~------------V~~v~~~~~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSC------------EEEEECCTTCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCC------------eEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            35678999999  5789999999999999997            566677778999999999999999999 69999884


Q ss_pred             ---Cc--eEEEcCCC
Q 013837          248 ---GV--AVRVRRPT  257 (435)
Q Consensus       248 ---g~--~l~v~~~~  257 (435)
                         |+  +|.|.+..
T Consensus        83 ~~~g~~~~ly~~~~~   97 (345)
T 3tht_A           83 DDLGQKITLYLNFVE   97 (345)
T ss_dssp             CTTSCEEECEEEECS
T ss_pred             cccCCceEEEEEEee
Confidence               44  67777753

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.07  E-value=4.6e-10  Score=99.80  Aligned_cols=79  Identities=14%  Similarity=0.123  Sum_probs=66.5

Q ss_pred             CCeEEEcCCC-----CCCCHHHHHHHHHhcCCeeEEEEeecCC----CCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe
Q 013837          294 PDRVFVGGLP-----YYFTETQIKELLESFGTLHGFDLVKDRD----TGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK  364 (435)
Q Consensus       294 ~~~l~V~nLp-----~~~te~~l~~~F~~~G~v~~v~i~~~~~----tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~  364 (435)
                      ...+.+.|+-     ..-.+++|.+.|++||.|..+.|+.+..    ++.++|++||+|.+.++|.+|+..|||.+|+|+
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            3456665552     2235689999999999999999986543    458999999999999999999999999999999


Q ss_pred             EEEEEEcc
Q 013837          365 TLTVRRAT  372 (435)
Q Consensus       365 ~l~V~~a~  372 (435)
                      .|.|.|+.
T Consensus       204 ~i~~~~~~  211 (222)
T 3dxb_A          204 KVVAEVYD  211 (222)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEcC
Confidence            99999984

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.06  E-value=2.5e-10  Score=88.35  Aligned_cols=73  Identities=18%  Similarity=0.124  Sum_probs=59.4

Q ss_pred             cCCeEEEcCC--CCCC--------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--------CCCcEEEEEecCHHH
Q 013837          173 HARRVYVGGL--PPLA--------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--------HEKKFAFVEMRTVEE  234 (435)
Q Consensus       173 ~~~~l~V~nl--p~~~--------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~--------~~~g~afv~f~~~~~  234 (435)
                      +++.|.|.|+  |..+        .+++|++.|++||.|..            +.+.        .++|||||+|.+.++
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~------------v~i~~~~~~~~~~~~G~~fV~f~~~~~   71 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKS------------IEIPRPVDGVEVPGCGKIFVEFTSVFD   71 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEE------------EECCCCBTTBCCTTTTEEEEEESSHHH
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEE------------EEEeccCCCCCcCCcEEEEEEECCHHH
Confidence            4678999998  3333        24789999999998543            3332        468999999999999


Q ss_pred             HHHHH-HhCCceecCceEEEcCCC
Q 013837          235 ASNAM-ALDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       235 a~~a~-~l~~~~~~g~~l~v~~~~  257 (435)
                      |.+|+ .|||..|.|+.|.|.+..
T Consensus        72 A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           72 CQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             HHHHHHHHTTCEETTEECEEEEEC
T ss_pred             HHHHHHHhCCCEeCCCEEEEEEeC
Confidence            99999 699999999999998753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=1.3e-09  Score=83.12  Aligned_cols=74  Identities=11%  Similarity=0.065  Sum_probs=57.4

Q ss_pred             CCeEEEcCCC-------CCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-cCCCcEEEEEecCHHHHHHHHHhCCce
Q 013837          174 ARRVYVGGLP-------PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-NHEKKFAFVEMRTVEEASNAMALDGII  245 (435)
Q Consensus       174 ~~~l~V~nlp-------~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-~~~~g~afv~f~~~~~a~~a~~l~~~~  245 (435)
                      ..+|.|.-..       ..+|+++|+++|.+||.|            ..+.+ +.++|||||+|.+.++|..|+.. +..
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V------------~~v~i~~~~rGfaFVeF~~~~~A~~Ai~~-~~~   76 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEV------------LNLVLSSKKPGTAVVEFATVKAAELAVQN-EVG   76 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCE------------EEEEEESSSSSEEEEEESCHHHHHHHHHT-CCB
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCE------------EEEEEccCCCCEEEEEECCHHHHHHHHHh-cCC
Confidence            3456665544       458999999999999985            33333 57899999999999999999953 344


Q ss_pred             ecCceEEEcCCCCCC
Q 013837          246 FEGVAVRVRRPTDYN  260 (435)
Q Consensus       246 ~~g~~l~v~~~~~~~  260 (435)
                      +.|++|.|.|+....
T Consensus        77 ~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           77 LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSSSBCEEECSSCCC
T ss_pred             CCCCeEEEEEccCCC
Confidence            689999999987553

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.02  E-value=4e-10  Score=82.82  Aligned_cols=73  Identities=14%  Similarity=0.169  Sum_probs=61.2

Q ss_pred             CCCCeEEEcCCCCC-----CCH----HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeC
Q 013837          292 EGPDRVFVGGLPYY-----FTE----TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMG  362 (435)
Q Consensus       292 ~~~~~l~V~nLp~~-----~te----~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~  362 (435)
                      .+..||+|..++..     +-.    .+|.+.|..||.|..++|+.++        +||+|.+.++|.+||+ |||..++
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            34458999887643     222    5688999999999999999873        9999999999999999 9999999


Q ss_pred             CeEEEEEEccC
Q 013837          363 DKTLTVRRATA  373 (435)
Q Consensus       363 g~~l~V~~a~~  373 (435)
                      |+.|+|++..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998643

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.98  E-value=1.3e-10  Score=89.75  Aligned_cols=66  Identities=17%  Similarity=0.315  Sum_probs=53.5

Q ss_pred             EcCCCCCCCHHHHHHHH------------HHHHHhhcCCCCCCCCceEEEEe-----cCCCcEEEEEecCHHHHHHHH-H
Q 013837          179 VGGLPPLANEQAIATFF------------SQVMTAIGGNSAGPGDAVVNVYI-----NHEKKFAFVEMRTVEEASNAM-A  240 (435)
Q Consensus       179 V~nlp~~~t~~~l~~~f------------~~~G~i~~~~~~~~~~~v~~~~~-----~~~~g~afv~f~~~~~a~~a~-~  240 (435)
                      +.|||..+++++|.+.|            ++||.|.            .+.+     +.++|||||+|.+.++|.+|+ .
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~------------~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~   87 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVE------------EMNVCDNLGDHLVGNVYVKFRREEDAEKAVID   87 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEE------------EEEECCSSSSSSEEEEEEEESCHHHHHHHHHH
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceE------------EEEEEeCCCCCccEEEEEEECCHHHHHHHHHH
Confidence            56777778887777666            9999854            3333     346899999999999999999 6


Q ss_pred             hCCceecCceEEEcCC
Q 013837          241 LDGIIFEGVAVRVRRP  256 (435)
Q Consensus       241 l~~~~~~g~~l~v~~~  256 (435)
                      |||..+.|++|.|.++
T Consensus        88 lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           88 LNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HTTCEETTEECCEEEC
T ss_pred             HCCCEECCEEEEEEEc
Confidence            9999999999999864

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.89  E-value=1.7e-09  Score=85.29  Aligned_cols=80  Identities=15%  Similarity=0.041  Sum_probs=61.6

Q ss_pred             ccCCeEEEcCCCC--C---CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHH-Hh
Q 013837          172 RHARRVYVGGLPP--L---ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-AL  241 (435)
Q Consensus       172 ~~~~~l~V~nlp~--~---~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~-~l  241 (435)
                      .++++|+|.|+-.  .   -.+++|++.|.+||.|..+.      ++.+...    +.++|||||+|.+.++|.+|+ .|
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~------I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~L   91 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVI------IYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL   91 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEE------EEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEE------EeecCCCcccCCcceEEEEEEECCHHHHHHHHHHH
Confidence            4688999999942  2   23789999999999975521      1111111    234699999999999999999 69


Q ss_pred             CCceecCceEEEcCCC
Q 013837          242 DGIIFEGVAVRVRRPT  257 (435)
Q Consensus       242 ~~~~~~g~~l~v~~~~  257 (435)
                      ||..|.|+.|.|.+..
T Consensus        92 nGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           92 NGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             TTCEETTEECEEEEEC
T ss_pred             CCCEECCcEEEEEEcC
Confidence            9999999999998754

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.85  E-value=3.9e-09  Score=82.60  Aligned_cols=73  Identities=15%  Similarity=0.193  Sum_probs=57.8

Q ss_pred             cCCeEEEcCCCCCC----------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe--cCCCcEEEEEecCHHHHHHHH-
Q 013837          173 HARRVYVGGLPPLA----------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVEMRTVEEASNAM-  239 (435)
Q Consensus       173 ~~~~l~V~nlp~~~----------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~--~~~~g~afv~f~~~~~a~~a~-  239 (435)
                      ++++|.|.|+=...          .+++|++.|++||.|..            +.+  ...+|||||+|.+.++|.+|+ 
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~------------v~i~~~~~~G~~fV~f~~~e~A~~Ai~   73 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIH------------IYVDKNSAQGNVYVKCPSIAAAIAAVN   73 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSE------------EEECTTCTTCCEEEECSSHHHHHHHHH
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEE------------EEEecCCCcEEEEEEECCHHHHHHHHH
Confidence            46678888874321          24688999999998643            333  235899999999999999999 


Q ss_pred             HhCCceecCceEEEcCCC
Q 013837          240 ALDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       240 ~l~~~~~~g~~l~v~~~~  257 (435)
                      .|||..|.|+.|.|.++.
T Consensus        74 ~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           74 ALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             HHTTCEETTEECEEEEEC
T ss_pred             HhCCCEECCEEEEEEEEc
Confidence            699999999999999764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.75  E-value=1.6e-08  Score=74.03  Aligned_cols=70  Identities=14%  Similarity=0.148  Sum_probs=55.7

Q ss_pred             CCeEEEcCCCC----CCCH----HHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCce
Q 013837          174 ARRVYVGGLPP----LANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGII  245 (435)
Q Consensus       174 ~~~l~V~nlp~----~~t~----~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~  245 (435)
                      .-||+|.-++.    ....    .+|.+.|.+||.            |+.+++...+  +||+|.+.++|.+|++|||..
T Consensus         7 d~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~------------Vi~vr~~~d~--~fVtF~d~~sAlaAi~mnG~~   72 (91)
T 2dnr_A            7 GGTVLVSIKSSLPENNFFDDALIDELLQQFASFGE------------VILIRFVEDK--MWVTFLEGSSALNVLSLNGKE   72 (91)
T ss_dssp             SCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCC------------EEEEEECSSS--EEEEESSHHHHHHGGGGTTCE
T ss_pred             CCeEEEEeccCccccccCCHHHHHHHHHHHHhCCC------------eEEEEEecCC--EEEEECChHHHHHHHhcCCeE
Confidence            44788877662    2323    668888999986            6666665544  899999999999999999999


Q ss_pred             ecCceEEEcCCC
Q 013837          246 FEGVAVRVRRPT  257 (435)
Q Consensus       246 ~~g~~l~v~~~~  257 (435)
                      +.|+.|+|+.++
T Consensus        73 v~Gr~LkV~lkt   84 (91)
T 2dnr_A           73 LLNRTITIALKS   84 (91)
T ss_dssp             ETTEEEEEEECC
T ss_pred             eCCeEEEEEeCC
Confidence            999999999765

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.72  E-value=1.7e-08  Score=78.98  Aligned_cols=72  Identities=10%  Similarity=0.034  Sum_probs=62.8

Q ss_pred             ccCCeEEEcCCCCC-CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecC-HHHHHHHH-Hh--CCcee
Q 013837          172 RHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT-VEEASNAM-AL--DGIIF  246 (435)
Q Consensus       172 ~~~~~l~V~nlp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~-~~~a~~a~-~l--~~~~~  246 (435)
                      ...+.|+|+||+.. ++.++|+++|+.||.            |..|.+......|||+|.+ ..+|..|+ .+  ++..|
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~------------V~~Vd~~~g~~tgfVrf~~~~~~A~~av~~ln~~~~~i   83 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQL   83 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCT
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCC------------EEEEEEecCCCEEEEEECCChHHHHHHHHHhhcCCcEE
Confidence            45788999999999 999999999999986            7778887788899999999 89999999 57  47889


Q ss_pred             cCceEEEcC
Q 013837          247 EGVAVRVRR  255 (435)
Q Consensus       247 ~g~~l~v~~  255 (435)
                      .|..+.+..
T Consensus        84 ~g~~~~~ev   92 (121)
T 1owx_A           84 RNKEVTWEV   92 (121)
T ss_dssp             TSSSEEEEE
T ss_pred             eCcEEEEEE
Confidence            998888864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.69  E-value=1.2e-07  Score=70.92  Aligned_cols=73  Identities=15%  Similarity=0.129  Sum_probs=67.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhc-----CCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESF-----GTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~-----G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      ..++|-+-|||..+++..|+.++++|     |.|..|.+..|.      |-|+|+|.+...|-+|.-+|+|..|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35789999999999999999999999     999999998874      3599999999999999999999999999999


Q ss_pred             EEEc
Q 013837          368 VRRA  371 (435)
Q Consensus       368 V~~a  371 (435)
                      |.-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            9865

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=3.4e-08  Score=72.60  Aligned_cols=71  Identities=23%  Similarity=0.280  Sum_probs=55.5

Q ss_pred             cCCeEEEcCCCCC-----CCH----HHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCC
Q 013837          173 HARRVYVGGLPPL-----ANE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDG  243 (435)
Q Consensus       173 ~~~~l~V~nlp~~-----~t~----~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~  243 (435)
                      +.-||+|.-++..     ...    .+|.+.|.+||+|            +.+++...+  +||+|.+.++|.+||+|||
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~V------------ilvr~v~d~--~fVtF~d~~sAl~AI~ldG   79 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTI------------VLVRINQGQ--MLVTFADSHSALSVLDVDG   79 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCC------------SEEEEETTE--EEEECSCSHHHHHHHHGGG
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCE------------EEEEEecCc--EEEEEcChHHHHHHHhcCC
Confidence            3458999888643     222    5688899999873            344544444  9999999999999999999


Q ss_pred             ceecCceEEEcCCC
Q 013837          244 IIFEGVAVRVRRPT  257 (435)
Q Consensus       244 ~~~~g~~l~v~~~~  257 (435)
                      ..++|+.|+|++..
T Consensus        80 ~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           80 MKVKGRAVKISGPS   93 (95)
T ss_dssp             SEETTEEEEEECCC
T ss_pred             eeeCCeEEEEeccC
Confidence            99999999998643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.44  E-value=1.1e-06  Score=65.79  Aligned_cols=76  Identities=14%  Similarity=0.209  Sum_probs=64.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|-|-|||..++...|+.|++++-.|.       ...+..+.+-.+.+=|+|+|.+...|-+|. +|+|.+|.|++
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~-------~g~i~KI~L~pDH~GAivef~d~~~AgKasLaL~G~ef~gr~   91 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHIN-------EKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQFQGKV   91 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCC-------TTTCSEEEEETTTTEEEEECSCHHHHHHHHHHHSSEEETTEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccC-------ccceeEEEEecCCCceEEEEccchhhHHHHhhcCCeeecCeE
Confidence            4578999999999999999999999993221       112556666677888999999999999998 89999999999


Q ss_pred             EEEc
Q 013837          251 VRVR  254 (435)
Q Consensus       251 l~v~  254 (435)
                      |.+.
T Consensus        92 Lr~g   95 (117)
T 2l9w_A           92 IRSG   95 (117)
T ss_dssp             EEEE
T ss_pred             EEec
Confidence            9997

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.26  E-value=4.6e-06  Score=62.04  Aligned_cols=74  Identities=19%  Similarity=0.261  Sum_probs=60.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..++|.|.|||..+.++.|.-+|+.--.       .-+..|..+....  +-|+|+|.+.+.|...|+-..+.|++..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rr-------sGGG~V~~v~~~~--~~AvItF~d~~va~rVL~k~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRR-------SGGGPVLSWQRLG--CGGVLTFREPADAERVLAQADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTT-------TCCCCEEEEEEET--TEEEEEESSHHHHHHHHTCSCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCc-------CCCceeeEEEEcC--CcEEEEEcChHHHHHHhcCCcceecCeEEE
Confidence            3578999999999999999999997200       0134577777655  889999999999999998878999999999


Q ss_pred             EcC
Q 013837          253 VRR  255 (435)
Q Consensus       253 v~~  255 (435)
                      |..
T Consensus        78 V~P   80 (104)
T 2dhx_A           78 LRP   80 (104)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            974

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.01  E-value=3.9e-06  Score=74.18  Aligned_cols=78  Identities=15%  Similarity=0.039  Sum_probs=56.0

Q ss_pred             CCeEEEcCCCC-----CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec----CCCcEEEEEecCHHHHHHHH-HhCC
Q 013837          174 ARRVYVGGLPP-----LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN----HEKKFAFVEMRTVEEASNAM-ALDG  243 (435)
Q Consensus       174 ~~~l~V~nlp~-----~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~----~~~g~afv~f~~~~~a~~a~-~l~~  243 (435)
                      ...+.+.|+-.     .-.+++|.+.|.+||.|....      ++.+...+    .++|++||+|.+.++|.+|+ .|||
T Consensus       124 s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~------v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~g  197 (222)
T 3dxb_A          124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVI------IYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG  197 (222)
T ss_dssp             CSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEE------EEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTT
T ss_pred             cccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEE------EecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcC
Confidence            34455555432     235688999999999864421      01111111    56799999999999999999 6999


Q ss_pred             ceecCceEEEcCCC
Q 013837          244 IIFEGVAVRVRRPT  257 (435)
Q Consensus       244 ~~~~g~~l~v~~~~  257 (435)
                      ..|.|++|.|.+..
T Consensus       198 r~~~gr~i~~~~~~  211 (222)
T 3dxb_A          198 RWFAGRKVVAEVYD  211 (222)
T ss_dssp             CBSSSSBCEEEECC
T ss_pred             ceECCeEEEEEEcC
Confidence            99999999998754

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.98  E-value=2.1e-05  Score=58.78  Aligned_cols=75  Identities=12%  Similarity=0.096  Sum_probs=63.1

Q ss_pred             CCCCeEEEcCCCCCC-C----HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          292 EGPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~-t----e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ..+++|+|.||+..+ +    .+.++++|..|+++......+.-      .=..|.|.++++|.+|-..||+..|.|+.|
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            345789999998765 2    25789999999998887776642      247899999999999999999999999999


Q ss_pred             EEEEcc
Q 013837          367 TVRRAT  372 (435)
Q Consensus       367 ~V~~a~  372 (435)
                      +|-|+.
T Consensus        77 r~YFgq   82 (104)
T 1wey_A           77 KLYFAQ   82 (104)
T ss_dssp             EEECCC
T ss_pred             EEEecC
Confidence            999995

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.85  E-value=9.2e-05  Score=54.50  Aligned_cols=78  Identities=14%  Similarity=0.175  Sum_probs=62.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcCHHHHHHHHHHhCCceeC---C--eEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMG---D--KTLT  367 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~--~~G~afV~f~~~~~A~~Al~~l~g~~~~---g--~~l~  367 (435)
                      ++|.|++||+.+||+++.+.+..+..+........+.+..  .-.-|||.|.+.+++....+.++|+.|-   |  ....
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~~a~   81 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEeeeE
Confidence            4799999999999999999999998877776666543322  2246999999999999999999999883   2  3456


Q ss_pred             EEEcc
Q 013837          368 VRRAT  372 (435)
Q Consensus       368 V~~a~  372 (435)
                      |+||-
T Consensus        82 VE~AP   86 (91)
T 1uw4_A           82 VEFAP   86 (91)
T ss_dssp             EEECS
T ss_pred             EEEcC
Confidence            77774

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.73  E-value=0.00019  Score=52.70  Aligned_cols=56  Identities=18%  Similarity=0.385  Sum_probs=47.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  356 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l  356 (435)
                      .....++| ++|..+...||.++|+.||.| .|..+-|.       -|||.|.+.+.|..|+..+
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            33456677 999999999999999999976 47777763       6999999999999999965

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.66  E-value=0.00063  Score=50.59  Aligned_cols=75  Identities=20%  Similarity=0.268  Sum_probs=61.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHh-----cCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLES-----FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~-----~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ...++|.|.|||..+.++.|.-+|+.     -|.|..+....        +-|+|+|.+.+.|+..|+ ...+.|.|..|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~-k~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLA-QADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHT-CSCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhc-CCcceecCeEE
Confidence            34579999999999999999999997     25687776643        368999999999999987 34789999999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      .|....+..
T Consensus        77 sV~P~~~~~   85 (104)
T 2dhx_A           77 SLRPAPPRA   85 (104)
T ss_dssp             EEEECCCCC
T ss_pred             EEEcCCCCC
Confidence            998765543

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.60  E-value=0.00028  Score=54.36  Aligned_cols=72  Identities=17%  Similarity=0.181  Sum_probs=59.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC-eEEEEEEc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD-KTLTVRRA  371 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g-~~l~V~~a  371 (435)
                      ..+.|.|-+.|... ...|...|++||.|++.....    +  ..+..|.|.+..+|++||. .||..|+| ..|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~----~--~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN----T--GNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS----S--SSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC----C--CCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            35689999999884 677889999999998777621    1  3478999999999999999 69999984 77888886


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.25  E-value=0.0012  Score=50.79  Aligned_cols=73  Identities=19%  Similarity=0.259  Sum_probs=59.6

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecC-c
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEG-V  249 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g-~  249 (435)
                      ......|.|-+.|+.. ...|...|.+||.|            +..........-.|.|.+..+|.+||..||..|.| .
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~I------------v~~~~~~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~   87 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNI------------LKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESI   87 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCE------------EEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcE------------EEeccCCCCCeEEEEeCCHHHHHHHHHhCCeEecCCE
Confidence            3457789999999986 57788999999984            44444556789999999999999999999999985 6


Q ss_pred             eEEEcCC
Q 013837          250 AVRVRRP  256 (435)
Q Consensus       250 ~l~v~~~  256 (435)
                      .|-|.+.
T Consensus        88 mIGV~p~   94 (119)
T 1wwh_A           88 MIGVKPC   94 (119)
T ss_dssp             ECEEEEC
T ss_pred             EEEEEEC
Confidence            6777654

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.21  E-value=0.00044  Score=51.69  Aligned_cols=73  Identities=11%  Similarity=0.018  Sum_probs=58.7

Q ss_pred             cCCeEEEcCCCCCC-CH----HHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          173 HARRVYVGGLPPLA-NE----QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       173 ~~~~l~V~nlp~~~-t~----~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      .+.+|+|.||+..+ +.    +.++++|..|+.            +.....-++-.-..|.|.++++|.+|- +|++..+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~------------~~tF~~lkSFRRirv~F~~~~~A~~AR~~Lh~~~f   71 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDK------------DTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF   71 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCS------------SCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCc------------CcceeecCcceEEEEEeCChHHHHHHHHHhcccee
Confidence            35689999998865 32    567888888865            333455556667899999999999999 7999999


Q ss_pred             cCceEEEcCCC
Q 013837          247 EGVAVRVRRPT  257 (435)
Q Consensus       247 ~g~~l~v~~~~  257 (435)
                      +|+.|+|-++.
T Consensus        72 ~g~~~r~YFgq   82 (104)
T 1wey_A           72 LGKEMKLYFAQ   82 (104)
T ss_dssp             TTEECEEECCC
T ss_pred             cCceeEEEecC
Confidence            99999999876

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.11  E-value=0.0006  Score=50.37  Aligned_cols=78  Identities=17%  Similarity=0.165  Sum_probs=54.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcCHHHHHHHHHHhCCceeCC-----eEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTLT  367 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~--~~G~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l~  367 (435)
                      -+|.|+.||+.+||+++.+.+..+-.+........+.+.+  .-.-|||.|.+.++.....+.++|..|-+     -...
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a~   89 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPAV   89 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeeeE
Confidence            4799999999999999877777654443322222222111  11348999999999999999999998832     3566


Q ss_pred             EEEcc
Q 013837          368 VRRAT  372 (435)
Q Consensus       368 V~~a~  372 (435)
                      |+||-
T Consensus        90 VE~AP   94 (97)
T 2l08_A           90 VEFAP   94 (97)
T ss_dssp             EEECC
T ss_pred             EEecC
Confidence            77773

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.02  E-value=0.0011  Score=48.87  Aligned_cols=53  Identities=19%  Similarity=0.410  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~  357 (435)
                      .++| ++|..+...||.++|+.||.| .|..+-|.       -|||.|.+.+.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            4556 999999999999999999954 57777763       69999999999999999764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.83  E-value=0.0013  Score=51.31  Aligned_cols=77  Identities=22%  Similarity=0.277  Sum_probs=56.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecC------------CCC-CcceEEEEEEcCHHHHHHHHHHhCCc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDR------------DTG-NSKGYGFCVYQDPAVTDIACAALNGL  359 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~-v~i~~~~------------~tg-~~~G~afV~f~~~~~A~~Al~~l~g~  359 (435)
                      ...|.|-+.|... ...|.+.|++||.|++ +.+..+.            -.+ ....+..|.|.+..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            3578888997664 4567789999999865 2211100            000 124578999999999999999 6999


Q ss_pred             eeCCeEEEEEEcc
Q 013837          360 KMGDKTLTVRRAT  372 (435)
Q Consensus       360 ~~~g~~l~V~~a~  372 (435)
                      .|+|..|-|....
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999999999883

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.30  E-value=0.0044  Score=45.47  Aligned_cols=64  Identities=16%  Similarity=0.308  Sum_probs=47.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~------~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      .+|.|++||+.+||+++.+.+..+..+          ......-|.      .-.-|||.|.+.+++.... .++|+.|.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~----------d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEH----------DYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCE----------EEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccc----------eEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            479999999999999999888876421          011111222      1258999999999999998 59999886


Q ss_pred             C
Q 013837          248 G  248 (435)
Q Consensus       248 g  248 (435)
                      +
T Consensus        72 D   72 (91)
T 1uw4_A           72 D   72 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.01  E-value=0.0042  Score=48.43  Aligned_cols=82  Identities=15%  Similarity=0.237  Sum_probs=56.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceE------EEEec--CCCcEEEEEecCHHHHHHHHHhCCce
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVV------NVYIN--HEKKFAFVEMRTVEEASNAMALDGII  245 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~------~~~~~--~~~g~afv~f~~~~~a~~a~~l~~~~  245 (435)
                      ...|.|-+.|...+ ..|.+.|++||.|+............      ..+..  .......|+|.+..+|.+||..||..
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            45689999977665 56888999999987632111000000      00011  13568899999999999999999999


Q ss_pred             ecCceEEEcCC
Q 013837          246 FEGVAVRVRRP  256 (435)
Q Consensus       246 ~~g~~l~v~~~  256 (435)
                      |.|.-|-|.+.
T Consensus        86 i~G~mIGV~Py   96 (132)
T 3p3d_A           86 FNGVLLGVIPY   96 (132)
T ss_dssp             ETTEECEEEEC
T ss_pred             eCcEEEEEEEC
Confidence            99997788754

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=95.61  E-value=0.016  Score=42.56  Aligned_cols=52  Identities=17%  Similarity=0.217  Sum_probs=41.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA  240 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~  240 (435)
                      ...++| ++|......||.++|..||.|          .|.=+    +-..|||.|.+++.|..||.
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv----------~I~Wi----dDTsAlvvf~~~~~a~~al~   67 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI----------QISWI----DDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC----------CCEEE----ETTEEEEECSCHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE----------EEEEE----cCCeEEEEecCHHHHHHHHH
Confidence            345666 999999999999999999843          12222    24689999999999999995

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.48  E-value=0.0077  Score=58.19  Aligned_cols=55  Identities=13%  Similarity=0.188  Sum_probs=41.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHH
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA  355 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~  355 (435)
                      +.|+|. .|..+++.+|.+.|++||+|..+.+.++.     .-||.|||.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            679997 68899999999999999999999887753     25999999999998877653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.39  E-value=0.012  Score=56.82  Aligned_cols=61  Identities=18%  Similarity=0.176  Sum_probs=42.0

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCC-cEEEEEecCHHHHHHHHHhCC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEK-KFAFVEMRTVEEASNAMALDG  243 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~-g~afv~f~~~~~a~~a~~l~~  243 (435)
                      .+...++|+|. .|..+++.+|.++|++||.|.            ++..-.++ -||.|||.+.+++..++...+
T Consensus        49 ~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~------------~~~~~~~~g~~~~vef~~~~~~~~~~~~~~  110 (464)
T 3pq1_A           49 REQAQRTVLIH-CPEKISENKFLKYLSQFGPIN------------NHFFYESFGLYAVVEFCQKESIGSLQNGTH  110 (464)
T ss_dssp             HHHHHTEEEEE-ECCC---CHHHHHHGGGSCCC------------CEEEECSSSEEEEEECC---CCHHHHSSCC
T ss_pred             HHHhcceEEEE-cCCCCCHHHHHHHHHhcCCcc------------eEEEEccCCeEEEEEeCCHHHHHHHHhccC
Confidence            34567899998 799999999999999999853            33333344 599999999999998874433

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=94.33  E-value=0.022  Score=41.98  Aligned_cols=51  Identities=20%  Similarity=0.231  Sum_probs=40.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA  240 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~  240 (435)
                      ..++| ++|......||.++|..||.|            ....+  +-..|||.|.+++.|..||.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv------------~I~Wi--dDTsAlvvf~~~~~a~~al~   57 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI------------QISWI--DDTSAFVSLSQPEQVKIAVN   57 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE------------EEEEE--ETTEEEEEEEEECHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE------------EEEEE--cCCeEEEEecCHHHHHHHHH
Confidence            34666 999999999999999999842            22222  24689999999999999995

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.96  E-value=0.03  Score=41.32  Aligned_cols=72  Identities=18%  Similarity=0.218  Sum_probs=46.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .+-+|.|+.||+.+||+++.+.+..+-.+ .....-+++.-.   -...-.-|||.|.+.++..... .++|..|.+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~-d~~~fv~G~~s~---~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAH-DYFEFFAADLSL---YPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSE-EECCCCCCCSSS---CCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCcc-ceEEEeCCccCC---CCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            35589999999999999987776654111 000000000000   0011257999999999999999 599988854

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=88.35  E-value=1.1  Score=44.08  Aligned_cols=55  Identities=18%  Similarity=0.390  Sum_probs=45.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN  357 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~  357 (435)
                      ...++|+ +|..+...+|.++|+.||.| .|..+-+       ..|||.|.+.+.|..++..++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHHH
Confidence            4567776 88899999999999999965 4555544       269999999999999999874

>1jmt_B Splicing factor U2AF 65 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens}

Probab=82.34  E-value=0.46  Score=25.92  Aligned_cols=16  Identities=19%  Similarity=0.397  Sum_probs=13.7

Q ss_pred             CCccCCCCccCCCCCC
Q 013837          112 SGFDMAPPAAAMLPGA  127 (435)
Q Consensus       112 ~~~~~~p~~~~~~~~~  127 (435)
                      ..||++|+||+++++.
T Consensus         6 ~~WDvpP~GyE~vtp~   21 (28)
T 1jmt_B            6 KYWDVPPPGFEHITPM   21 (28)
T ss_dssp             CCBTCCCTTCTTSCHH
T ss_pred             cccCCCCCCccccCHH
Confidence            3799999999998864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	435
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-17
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-16
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-15
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-08
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-15
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	2e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	6e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-14
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-13
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-06
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-11
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-13
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-08
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	4e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-13
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-12
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.003
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-06
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-12
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-07
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-12
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	3e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	8e-10
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-12
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-05
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	4e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-06
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	7e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-06
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	7e-12
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-06
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	8e-12
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	2e-11
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-04
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	8e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	4e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	9e-05
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	5e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-11
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	8e-11
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-06
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-04
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-09
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-08
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	8e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-09
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	0.001
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-08
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	2e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-06
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	5e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	2e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	5e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	0.002
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.002
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.002
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.002

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.3 bits (189), Expect = 3e-17
 Identities = 41/212 (19%), Positives = 73/212 (34%), Gaps = 35/212 (16%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
             R++++GGL     ++++ + F Q  T            + +      + F FV   TV
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV------MRDPNTKRSRGFGFVTYATV 58

Query: 233 EEASNAMALDGIIFEGVAVRVRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAE 292
           EE   AM       +G  V  +R      +                          G   
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKRAVSREDS-----------------------QRPGAHL 95

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
              ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    D  
Sbjct: 96  TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI 155

Query: 353 CAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
                   +      VR+A      SK E  S
Sbjct: 156 V-IQKYHTVNGHNCEVRKA-----LSKQEMAS 181

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (101), Expect = 1e-05
 Identities = 14/95 (14%), Positives = 29/95 (30%), Gaps = 6/95 (6%)

Query: 161 MPVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH 220
                    A    ++++VGG+     E  +  +F Q             + + +     
Sbjct: 84  SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY------GKIEVIEIMTDRGSGK 137

Query: 221 EKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           ++ FAFV     +     +        G    VR+
Sbjct: 138 KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.6 bits (180), Expect = 5e-17
 Identities = 43/89 (48%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           ARR+YVG +P    E+A+  FF+  M   G   A PG+ V+ V IN +K FAF+E R+V+
Sbjct: 1   ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 234 EASNAMALDGIIFEGVAVRVRRPTDYNPT 262
           E + AMA DGIIF+G ++++RRP DY P 
Sbjct: 60  ETTQAMAFDGIIFQGQSLKIRRPHDYQPL 88

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.8 bits (144), Expect = 4e-12
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDL-----VKDRDTGNSKGYGFCVYQDPAVTD 350
           R++VG +P+  TE  + +   +   L G        V        K + F  ++    T 
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 351 IACAALNGLKMGDKTLTVRRA 371
            A  A +G+    ++L +RR 
Sbjct: 63  QAM-AFDGIIFQGQSLKIRRP 82

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (173), Expect = 5e-16
 Identities = 45/83 (54%), Positives = 58/83 (69%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGLP Y  + Q+KELL SFG L  F+LVKD  TG SKGY FC Y D  VTD A A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           LNG+++GDK L V+RA+  +  +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAKNA 85

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 1e-08
 Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           A ++++GGLP   N+  +    +              + V +      K +AF E   + 
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSF------GPLKAFNLVKDSATGLSKGYAFCEYVDIN 54

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
               A+  L+G+      + V+R
Sbjct: 55  VTDQAIAGLNGMQLGDKKLLVQR 77

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.3 bits (169), Expect = 2e-15
 Identities = 16/86 (18%), Positives = 32/86 (37%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           GA  G  GP  + V  +P+  +  +I +    +  + G   +K  + G   G     ++ 
Sbjct: 1   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 60

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRA 371
                 A   LN   +G + + +   
Sbjct: 61  RDEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.4 bits (167), Expect = 4e-15
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACA 354
           ++ V  +P+   + +I+EL  +FG L    L K    TG  +G+GF  +        A  
Sbjct: 10  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 355 AL-NGLKMGDKTLTVRRATA 373
           AL +   +  + L +  A +
Sbjct: 70  ALCHSTHLYGRRLVLEWADS 89

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 4e-08
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 7/86 (8%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           +   ++ V  +P  AN++ I   FS       G                 + F FV+  T
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTF-----GELKTVRLPKKMTGTGAHRGFGFVDFIT 60

Query: 232 VEEASNAMA--LDGIIFEGVAVRVRR 255
            ++A  A           G  + +  
Sbjct: 61  KQDAKKAFNALCHSTHLYGRRLVLEW 86

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 67.3 bits (164), Expect = 6e-15
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  ++E    FG +    +++D  T  S+G+GF  + D A  D    A
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD-KVLA 60

Query: 356 LNGLKMGDKTLTVRRA 371
            +  ++  KT+  + A
Sbjct: 61  QSRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.7 bits (126), Expect = 9e-10
 Identities = 9/80 (11%), Positives = 24/80 (30%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++++GGL     ++ +  +F Q               + +      + F FV        
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQF------GEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 55

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              +A      +   +  + 
Sbjct: 56  DKVLAQSRHELDSKTIDPKV 75

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.5 bits (162), Expect = 1e-14
 Identities = 18/76 (23%), Positives = 32/76 (42%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           ++VG L    TE  + E     G +    + +D  T  S GY +  +Q PA  + A   +
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 357 NGLKMGDKTLTVRRAT 372
           N   +  K + +  + 
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 3e-06
 Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 7/79 (8%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +YVG L P   E  +   FS     +            ++       +A+V  +   +A 
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAE 56

Query: 237 NAM-ALDGIIFEGVAVRVR 254
            A+  ++  + +G  VR+ 
Sbjct: 57  RALDTMNFDVIKGKPVRIM 75

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 65.7 bits (160), Expect = 3e-14
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 2/78 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  LP   T+ Q+  +   +G++   ++++D+ TG  +G  F  Y        A +A
Sbjct: 8   NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 356 LNG--LKMGDKTLTVRRA 371
           LN    + G + L+VR A
Sbjct: 68  LNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +YV  LP    +  + T F +  + +  N                +  AFV     EE
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLT------GRPRGVAFVRYNKREE 60

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A+ AL+ +I EG +  + 
Sbjct: 61  AQEAISALNNVIPEGGSQPLS 81

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.8 bits (160), Expect = 3e-14
 Identities = 25/80 (31%), Positives = 40/80 (50%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+VGGL    +E  + EL    G +    + KDR TG  +GYGF  +      D A   
Sbjct: 11  TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 356 LNGLKMGDKTLTVRRATASS 375
           ++ +K+  K + V +A+A +
Sbjct: 71  MDMIKLYGKPIRVNKASAHN 90

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.0 bits (106), Expect = 6e-07
 Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             VYVGGL    +E  +   F Q    +  +         +      + + FVE  + E+
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEED 63

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPTDYNPTL 263
           A  A+  +D I   G  +RV + + +N  L
Sbjct: 64  ADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (157), Expect = 5e-14
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  T+  +K+    FG +    L  D  TG S+G+GF ++++    D     
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD-KVMD 59

Query: 356 LNGLKMGDKTLTVRRA 371
               K+  K +  +RA
Sbjct: 60  QKEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.5 bits (136), Expect = 4e-11
 Identities = 12/80 (15%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++++GGL     ++ +  +FS+    +                   + F FV  +  E  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPIT------GRSRGFGFVLFKESESV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              M        G  +  +R
Sbjct: 55  DKVMDQKEHKLNGKVIDPKR 74

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 63.9 bits (155), Expect = 1e-13
 Identities = 21/77 (27%), Positives = 36/77 (46%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  LP   T+ ++  L  + G ++   +++D  TG S GY F  +     +  A   
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG+ + +K L V  A 
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 41.5 bits (97), Expect = 8e-06
 Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            + V  LP    ++ +   F  +              + +    +   +AFV+  +  ++
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPIN------TCRIMRDYKTGYSYGYAFVDFTSEMDS 57

Query: 236 SNAM-ALDGIIFEGVAVRVRR 255
             A+  L+GI      ++V  
Sbjct: 58  QRAIKVLNGITVRNKRLKVSY 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 2e-13
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGG+     E  +++  E +G +   +++ DR +G  +G+ F  + D    D     
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD-KIVI 62

Query: 356 LNGLKMGDKTLTVRRA 371
                +      VR+A
Sbjct: 63  QKYHTVNGHNCEVRKA 78

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           ++++VGG+     E  +  +F Q             + + +     ++ FAFV     + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIE------VIEIMTDRGSGKKRGFAFVTFDDHDS 56

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
               +        G    VR+
Sbjct: 57  VDKIVIQKYHTVNGHNCEVRK 77

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 2e-13
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           E   ++F+GGL +  T+  ++   E +GTL    +++D +T  S+G+GF  Y      D 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 352 ACAALNGLKMGDKTLTVRRATA 373
           A  A    K+  + +  +RA +
Sbjct: 64  AMNA-RPHKVDGRVVEPKRAVS 84

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV 232
             R++++GGL     ++++ + F Q        +      + +      + F FV   TV
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQW------GTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 233 EEASNAMALDGIIFEGVAVRVRR 255
           EE   AM       +G  V  +R
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKR 81

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.2 bits (153), Expect = 2e-13
 Identities = 30/79 (37%), Positives = 41/79 (51%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  LP   T+ + + L  S G +    LV+D+ TG S GYGF  Y DP   + A   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 356 LNGLKMGDKTLTVRRATAS 374
           LNGL++  KT+ V  A  S
Sbjct: 64  LNGLRLQTKTIKVSYARPS 82

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 9/86 (10%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V  LP    ++   + F  +                         + FV     ++
Sbjct: 3   TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKIT------GQSLGYGFVNYIDPKD 56

Query: 235 ASNAM-ALDGIIFEGVAVRVR--RPT 257
           A  A+  L+G+  +   ++V   RP+
Sbjct: 57  AEKAINTLNGLRLQTKTIKVSYARPS 82

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 3/96 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++  LPY  T  ++ ++   +G +         +T  ++G  + VY+D      AC  L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQH 392
           +G  + ++ L V    A+    K + +    Q +  
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLL 102

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 4e-08
 Identities = 15/81 (18%), Positives = 26/81 (32%), Gaps = 10/81 (12%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +Y+  LP     + +   F +          GP   +        +  A+V    + +
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKY---------GPIRQIRVGNTPETRGTAYVVYEDIFD 58

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A NA   L G       + V 
Sbjct: 59  AKNACDHLSGFNVCNRYLVVL 79

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.3 bits (151), Expect = 4e-13
 Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL     E +I+E    FG +   +L  D  T   +G+ F  +++          
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 356 LNGLKMGDKTLTVRRA 371
                +G     ++ A
Sbjct: 61  -KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.2 bits (130), Expect = 3e-10
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VGGL P   E+ I  +F               +  ++   N  + F F+  +  E  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGF------GEVESIELPMDNKTNKRRGFCFITFKEEEPV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
              M             ++ 
Sbjct: 55  KKIMEKKYHNVGLSKCEIKV 74

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.9 bits (150), Expect = 8e-13
 Identities = 20/76 (26%), Positives = 34/76 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VG L +Y TE QI EL    G +    +  D+    + G+ F  Y   A  + A   
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG ++ D+ +     
Sbjct: 69  INGTRLDDRIIRTDWD 84

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.9 bits (124), Expect = 3e-09
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 7/87 (8%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++  + +  +YVG L     E+ I   FS+                ++        F FV
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIK------KIIMGLDKMKKTACGFCFV 54

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRV 253
           E  +  +A NAM  ++G   +   +R 
Sbjct: 55  EYYSRADAENAMRYINGTRLDDRIIRT 81

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 2e-12
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 7/84 (8%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++++G L    T   +++L                      GY F  Y D      A   
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 356 LNG-LKMGDKTLTVRRATASSGQS 378
           L+G +++  K + V  + +   +S
Sbjct: 57  LSGKVELHGKIMEVDYSVSKKLRS 80

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (78), Expect = 0.003
 Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 14/82 (17%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++Y+G L P      +   F                  +   +  +  +AFV+      A
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKL------------PLAGQVLLKSGYAFVDYPDQNWA 50

Query: 236 SNAM-ALDG-IIFEGVAVRVRR 255
             A+  L G +   G  + V  
Sbjct: 51  IRAIETLSGKVELHGKIMEVDY 72

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.3 bits (146), Expect = 2e-12
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++ V  L +  ++  I+EL   FGTL    +  DR +G S G     ++  A    A   
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 60

Query: 356 LNGLKMGDKTLTVRRATA 373
            NG+ +  + + ++  T+
Sbjct: 61  YNGVPLDGRPMNIQLVTS 78

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 8/80 (10%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           ++ V  L    ++  I   F++  T            V           A V      +A
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAA-------VHYDRSGRSLGTADVHFERKADA 54

Query: 236 SNAM-ALDGIIFEGVAVRVR 254
             AM   +G+  +G  + ++
Sbjct: 55  LKAMKQYNGVPLDGRPMNIQ 74

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.8 bits (147), Expect = 2e-12
 Identities = 24/90 (26%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG       P R+ V  +P+ F +  ++++   FG +   D+    +   SKG+GF  +
Sbjct: 1   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--DVEIIFNERGSKGFGFVTF 58

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATA 373
           ++ A  D A   L+G  +  + + V  ATA
Sbjct: 59  ENSADADRAREKLHGTVVEGRKIEVNNATA 88

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 17/88 (19%), Positives = 29/88 (32%), Gaps = 9/88 (10%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           ++    +R++V  +P    +  +   F Q             D  +       K F FV 
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGK--------ILDVEIIFNERGSKGFGFVT 57

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRR 255
                +A  A   L G + EG  + V  
Sbjct: 58  FENSADADRAREKLHGTVVEGRKIEVNN 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V GLP   T+ ++++L   +G +    ++ D+ TG S+G GF  +      + A   
Sbjct: 8   NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 356 LNGLKMGDKT--LTVRRA 371
           LNG K    T  +TV+ A
Sbjct: 68  LNGQKPSGATEPITVKFA 85

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +YV GLP    ++ +   FSQ      G        V  V     +   F+      E
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQY-----GRIITSRILVDQVTGVS-RGVGFIRFDKRIE 60

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A+  L+G    G    + 
Sbjct: 61  AEEAIKGLNGQKPSGATEPIT 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.4 bits (146), Expect = 2e-12
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 298 FVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD---TGNSKGYGFCVYQDPAVTDIACA 354
           F+  L +  TE  +K +    G +    + K ++      S G+GF  Y+ P     A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 355 ALNGLKMGDKTLTVRRATASS 375
            L G  +    L VR +  ++
Sbjct: 62  QLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.9 bits (111), Expect = 1e-07
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 4/79 (5%)

Query: 178 YVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASN 237
           ++  L     E+ +   FS+V        +   +      +     F FVE +  E+A  
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKN---KAGVLLSMGFGFVEYKKPEQAQK 58

Query: 238 AM-ALDGIIFEGVAVRVRR 255
           A+  L G   +G  + VR 
Sbjct: 59  ALKQLQGHTVDGHKLEVRI 77

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.4 bits (146), Expect = 3e-12
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V GLP+  TE  +KE   +FG +    + KD  TG+SKG+GF  + +        + 
Sbjct: 10  DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQE 383
            + +    +    +        SK  Q+
Sbjct: 70  RHMI--DGRWCDCKLP-----NSKQSQD 90

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 2e-07
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 7/91 (7%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++A +    + V GLP    EQ +  +FS     +            ++   H K F FV
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVL------MVQVKKDLKTGHSKGFGFV 55

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRRPTD 258
                E     M+    + +G     + P  
Sbjct: 56  RFTEYETQVKVMS-QRHMIDGRWCDCKLPNS 85

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.5 bits (146), Expect = 3e-12
 Identities = 24/91 (26%), Positives = 40/91 (43%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G  R+FV  L Y  +E  +++L  ++G L       D  T   KG+ F  +  P   
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSKT 380
             A A ++G     + L V  +T     S++
Sbjct: 64  VKAYAEVDGQVFQGRMLHVLPSTIKKEASQS 94

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.7 bits (92), Expect = 6e-05
 Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
           + R++V  L   ++E+ +   FS        +                K FAFV     E
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL------TKKPKGFAFVTFMFPE 61

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
            A  A   +DG +F+G  + V  
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLP 84

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 59.7 bits (144), Expect = 3e-12
 Identities = 19/76 (25%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL    T   +K   E FG +    L+ D+ T   +G+GF  ++   + +  C  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 356 LNGLKMGDKTLTVRRA 371
           ++  ++ +K +  ++A
Sbjct: 60  IHFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 8e-10
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 6/80 (7%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           +++VGGL      + +  +F Q               + +   N  + F FV   + +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVD------DAMLMFDKTTNRHRGFGFVTFESEDIV 54

Query: 236 SNAMALDGIIFEGVAVRVRR 255
                +         V  ++
Sbjct: 55  EKVCEIHFHEINNKMVECKK 74

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 3e-12
 Identities = 24/80 (30%), Positives = 35/80 (43%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + V  L     ET ++EL   FG++    L KD+ TG SKG+ F  +        A A 
Sbjct: 10  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 69

Query: 356 LNGLKMGDKTLTVRRATASS 375
           ++G       L V  A  S+
Sbjct: 70  VSGFGYDHLILNVEWAKPST 89

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.0 bits (98), Expect = 7e-06
 Identities = 13/82 (15%), Positives = 26/82 (31%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V  L     E  +   F    +              +      K FAF+     E+
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYL------AKDKTTGQSKGFAFISFHRRED 62

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A+ A+  + G  ++ + + V  
Sbjct: 63  AARAIAGVSGFGYDHLILNVEW 84

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 3e-12
 Identities = 15/76 (19%), Positives = 31/76 (40%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++VGGL     +  +      FG +    +  D +T   +G+ F  ++       A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66

Query: 356 LNGLKMGDKTLTVRRA 371
           +N  ++  +T+ V  A
Sbjct: 67  MNESELFGRTIRVNLA 82

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 1e-05
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R +YVGGL    +++ +   F                  ++      + FAFVE    E+
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAED 59

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A+ A+  ++     G  +RV  
Sbjct: 60  AAAAIDNMNESELFGRTIRVNL 81

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 4e-12
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++F+GGL +  TE  ++   E +G L    +++D  +  S+G+GF  +   A  D A  A
Sbjct: 22  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-A 80

Query: 356 LNGLKMGDKTLTVRRATA 373
                +  + +  +RA A
Sbjct: 81  ARPHSIDGRVVEPKRAVA 98

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 2e-09
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 6/88 (6%)

Query: 168 QQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           ++     R++++GGL     E+++  ++ Q               + +      + F FV
Sbjct: 14  KREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV------MRDPASKRSRGFGFV 67

Query: 228 EMRTVEEASNAMALDGIIFEGVAVRVRR 255
              ++ E   AMA      +G  V  +R
Sbjct: 68  TFSSMAEVDAAMAARPHSIDGRVVEPKR 95

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.1 bits (145), Expect = 4e-12
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 4/80 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGF--DLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           R+F+GG+P      +I E +                 D   ++G+ F  Y+      +A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 354 AALNG--LKMGDKTLTVRRA 371
             L    +++    + V  A
Sbjct: 63  RKLMPGRIQLWGHQIAVDWA 82

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 5e-06
 Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 7/83 (8%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
           R+++GG+P +   + I    ++    +                   + FAFVE  +   A
Sbjct: 3   RLFIGGIPKMKKREEILEEIAK----VTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 58

Query: 236 SNA---MALDGIIFEGVAVRVRR 255
           + A   +    I   G  + V  
Sbjct: 59  AMARRKLMPGRIQLWGHQIAVDW 81

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 4e-12
 Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLV-KDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           +F+G L     E  + +   +FG +     + +D DTGNSKGY F  +     +D A  A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 356 LNGLKMGDKTLTVRRAT 372
           +NG  + ++ +TV  A 
Sbjct: 61  MNGQYLCNRPITVSYAF 77

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 14/80 (17%), Positives = 32/80 (40%), Gaps = 6/80 (7%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +++G L P  +E+ +   FS       G        + +    + K +AF+   + + + 
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAF-----GVILQTPKIMRDPDTGNSKGYAFINFASFDASD 55

Query: 237 NAM-ALDGIIFEGVAVRVRR 255
            A+ A++G       + V  
Sbjct: 56  AAIEAMNGQYLCNRPITVSY 75

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 5e-12
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 289 GGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G    PD    + V GL  Y TE  ++E+   +G +    +V D+ +  S+G+ F  +++
Sbjct: 1   GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 346 PAVTDIACAALNGLKMGDKTLTV 368
                 A    NG+++  + + V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 14/80 (17%), Positives = 27/80 (33%), Gaps = 7/80 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             + V GL     E+ +   FS+       +      +  +           V    V++
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF------VYFENVDD 63

Query: 235 ASNAM-ALDGIIFEGVAVRV 253
           A  A    +G+  +G  +RV
Sbjct: 64  AKEAKERANGMELDGRRIRV 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 7e-12
 Identities = 12/81 (14%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLES-FGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
            +++  L     + ++K+ L + F        +    +   +G  F ++++ +    A  
Sbjct: 5   TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 64

Query: 355 ALNGLKMGDKTLTVRRATASS 375
           ++ G    DK + ++ A   S
Sbjct: 65  SMQGFPFYDKPMRIQYAKTDS 85

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 14/89 (15%)

Query: 172 RHARRVYVGGLPPLANEQAI----ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFV 227
           R    +Y+  L     +  +       FS+               ++       +  AFV
Sbjct: 1   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFG---------QILDILVSRSLKMRGQAFV 51

Query: 228 EMRTVEEASNAM-ALDGIIFEGVAVRVRR 255
             + V  A+NA+ ++ G  F    +R++ 
Sbjct: 52  IFKEVSSATNALRSMQGFPFYDKPMRIQY 80

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 7e-12
 Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
           P  ++VG L    TE  I +L    G           +  ++  Y F  + +      A 
Sbjct: 8   PRTLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 65

Query: 354 AALNGLKMGDKTLTVRRATASSGQ 377
           AA+NG K+  K + V  AT  S Q
Sbjct: 66  AAMNGRKILGKEVKVNWATTPSSQ 89

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 6e-06
 Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 9/85 (10%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
              R +YVG L     E  I   FSQ+               +         + FVE   
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCK--------SCKMITEHTSNDPYCFVEFYE 57

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRR 255
             +A+ A+ A++G    G  V+V  
Sbjct: 58  HRDAAAALAAMNGRKILGKEVKVNW 82

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.0 bits (142), Expect = 8e-12
 Identities = 24/80 (30%), Positives = 45/80 (56%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGL +   E  ++++   +G +    +VKDR+T  S+G+GF  +++      A  A
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 356 LNGLKMGDKTLTVRRATASS 375
           +NG  +  + + V +A  SS
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 1e-05
 Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 7/83 (8%)

Query: 174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
             +++VGGL    NEQ++   FS+               V +      + F FV    ++
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVV------VKDRETQRSRGFGFVTFENID 58

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
           +A +AM A++G   +G  +RV +
Sbjct: 59  DAKDAMMAMNGKSVDGRQIRVDQ 81

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.6 bits (141), Expect = 2e-11
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 3/94 (3%)

Query: 285 SGAIGG-AEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
            GA G   EGP+   +F+  LP  F +  + ++   FG +    +  D+ T  SK +GF 
Sbjct: 6   IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 65

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRATASS 375
            Y +P     A  ++NG ++G K L V+   + +
Sbjct: 66  SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +++  LP    +Q +   F      +           ++   N  K F FV       
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVV------SAKVFIDKQTNLSKCFGFVSYDNPVS 72

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A  A+ +++G       ++V+ 
Sbjct: 73  AQAAIQSMNGFQIGMKRLKVQL 94

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.5 bits (138), Expect = 3e-11
 Identities = 18/85 (21%), Positives = 28/85 (32%), Gaps = 8/85 (9%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLV--------KDRDTGNSKGYGFCVYQDPA 347
            ++V GL    T   + +  +  G +               D++TG  KG     Y+DP 
Sbjct: 10  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 69

Query: 348 VTDIACAALNGLKMGDKTLTVRRAT 372
               A    +G       L V  A 
Sbjct: 70  TAKAAVEWFDGKDFQGSKLKVSLAR 94

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 20/90 (22%), Positives = 28/90 (31%), Gaps = 3/90 (3%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK--FAFVEMRTV 232
             +YV GL        +A FF Q          G     + +     K    A V     
Sbjct: 9   SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 233 EEASNAM-ALDGIIFEGVAVRVRRPTDYNP 261
             A  A+   DG  F+G  ++V       P
Sbjct: 69  PTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.9 bits (137), Expect = 4e-11
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 6/83 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           R+FVG LP   TE ++++L E +G      + KD+       +GF   +   + +IA   
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           L+ + +  K L VR A  S+  +
Sbjct: 64  LDNMPLRGKQLRVRFACHSASLT 86

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.7 bits (113), Expect = 8e-08
 Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 13/84 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VG LPP   E+ +   F +                  V+I+ +K F F+ + T   
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTL 56

Query: 235 ASNAM-ALDGIIFEGVAVRVRRPT 257
           A  A   LD +   G  +RVR   
Sbjct: 57  AEIAKVELDNMPLRGKQLRVRFAC 80

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 4e-11
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VF   L        +++   + G +    ++ DR++  SKG  +  + +          
Sbjct: 20  TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP-LAIG 78

Query: 356 LNGLKMGDKTLTVRRATA 373
           L G ++    + V+ + A
Sbjct: 79  LTGQRLLGVPIIVQASQA 96

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 5e-09
 Identities = 21/94 (22%), Positives = 35/94 (37%), Gaps = 7/94 (7%)

Query: 162 PVQVMTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHE 221
           PV  ++ +  R AR V+   L      + +  FFS V              + +      
Sbjct: 7   PVDNLSPEE-RDARTVFCMQLAARIRPRDLEDFFSAVGKVR------DVRIISDRNSRRS 59

Query: 222 KKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR 255
           K  A+VE   ++    A+ L G    GV + V+ 
Sbjct: 60  KGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQA 93

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 5e-11
 Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 5/90 (5%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
             G I G  G +  R++VG LP       I+++   +G       +  ++      + F 
Sbjct: 2   GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYG---AIRDIDLKNRRGGPPFAFV 58

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
            ++DP   + A    +G       L V   
Sbjct: 59  EFEDPRDAEDAVYGRDGYDYDGYRLRVEFP 88

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 9e-05
 Identities = 23/87 (26%), Positives = 34/87 (39%), Gaps = 10/87 (11%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A  +  R+YVG LPP    + I   F +          G    +          FAFVE 
Sbjct: 10  AGNNDCRIYVGNLPPDIRTKDIEDVFYKY---------GAIRDIDLKNRRGGPPFAFVEF 60

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRR 255
               +A +A+   DG  ++G  +RV  
Sbjct: 61  EDPRDAEDAVYGRDGYDYDGYRLRVEF 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 56.7 bits (136), Expect = 5e-11
 Identities = 23/77 (29%), Positives = 34/77 (44%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +FV  +     E +I+E    +G +    L  DR TG SKGY    Y+       A  A
Sbjct: 9   ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 68

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++  +T+ V    
Sbjct: 69  LNGAEIMGQTIQVDWCF 85

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 7/88 (7%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
           Q +     ++V  +   A E  I   F                  ++      K +A VE
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIK------NIHLNLDRRTGFSKGYALVE 55

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRVRR 255
             T ++A  A  AL+G    G  ++V  
Sbjct: 56  YETHKQALAAKEALNGAEIMGQTIQVDW 83

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 6e-11
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIA 352
           G   +F+  L        + +   +FG +    +V D +   SKGYGF  ++     + A
Sbjct: 7   GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 64

Query: 353 CAALNGLKMGDKTLTVRRAT 372
              +NG+ + D+ + V R  
Sbjct: 65  IEKMNGMLLNDRKVFVGRFK 84

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 6e-06
 Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)

Query: 176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEA 235
            +++  L    + +A+   FS                 V    N  K + FV   T E A
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGN--------ILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 236 SNAM-ALDGIIFEGVAVRVRR 255
             A+  ++G++     V V R
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGR 82

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 7e-11
 Identities = 17/83 (20%), Positives = 30/83 (36%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++  L    TE  +  L   F    G  +     TG  +G  F  + +  +   A   
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
           +NG K+  K L +        +S
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQRS 102

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.7 bits (136), Expect = 8e-11
 Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 1/96 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG+      P   F+G LPY  TE  IKE              +  +    KG+G+  +
Sbjct: 5   SSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRATASSGQSK 379
           +D      +  +LN   +G+K + V  A  +  +  
Sbjct: 65  EDLDSLL-SALSLNEESLGNKRIRVDVADQAQDKDS 99

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 2e-06
 Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
              ++G LP    E++I  FF  +  +                    K F + E   ++ 
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISA------VRLPREPSNPERLKGFGYAEFEDLDS 69

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
             +A++L+        +RV  
Sbjct: 70  LLSALSLNEESLGNKRIRVDV 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           ++FVGGLPY+ T+  +++  E FG +    ++ DR TG S+GYGF    D A  + AC  
Sbjct: 12  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 356 LNGLKMGDKTLTVRRATASS 375
            N   +  +   V  A   +
Sbjct: 72  PNP-IIDGRKANVNLAYLGA 90

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 6/81 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            +++VGGLP    + ++  +F                 + +      + + FV M     
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGF------GDIEEAVVITDRQTGKSRGYGFVTMADRAA 64

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
           A  A      I +G    V  
Sbjct: 65  AERACKDPNPIIDGRKANVNL 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 55.4 bits (133), Expect = 1e-10
 Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +    L +  TE ++KE+ E    +           G SKG  +  ++  A  +     
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 356 LNGLKMGDKTLTVRRATASSGQS 378
             G ++  +++++       G  
Sbjct: 73  KQGAEIDGRSVSLYYTGEKGGTR 95

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 46.2 bits (109), Expect = 3e-07
 Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 12/89 (13%)

Query: 167 TQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAF 226
           T +  R AR +    L     E  +   F   +     +  G             K  A+
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDG-----------KSKGIAY 57

Query: 227 VEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           +E ++  +A   +    G   +G +V + 
Sbjct: 58  IEFKSEADAEKNLEEKQGAEIDGRSVSLY 86

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.2 bits (130), Expect = 4e-10
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 13/89 (14%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 225
           +  Q++     VY GG+     +Q +   FS                ++ + +  EK ++
Sbjct: 10  VVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYS 57

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRV 253
           FV   T E A++A+ +++G   EG  V+ 
Sbjct: 58  FVRFSTHESAAHAIVSVNGTTIEGHVVKC 86

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.7 bits (121), Expect = 8e-09
 Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V+ GG+    T+  +++    FG +    +  ++       Y F  +        A  +
Sbjct: 20  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVS 73

Query: 356 LNGLKMGDKTLTVRRA 371
           +NG  +    +     
Sbjct: 74  VNGTTIEGHVVKCYWG 89

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 53.3 bits (127), Expect = 6e-10
 Identities = 13/76 (17%), Positives = 29/76 (38%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            +++   P  +T+  I++LL+    +     +       S+ + +               
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 356 LNGLKMGDKTLTVRRA 371
           LNGLK+   TL  + +
Sbjct: 63  LNGLKIEGYTLVTKVS 78

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 37.1 bits (85), Expect = 4e-04
 Identities = 13/81 (16%), Positives = 35/81 (43%), Gaps = 7/81 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             +++   PP   ++ I      +      N       + ++  N  ++FA++++ + E+
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDI------NVVALSIRLPSLRFNTSRRFAYIDVTSKED 55

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A   +  L+G+  EG  +  +
Sbjct: 56  ARYCVEKLNGLKIEGYTLVTK 76

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.7 bits (129), Expect = 7e-10
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 9/78 (11%)

Query: 296 RVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA 354
           RVF+G L      ++ ++ +   +G +              KG+ F  Y +      A A
Sbjct: 17  RVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFAFVQYVNERNARAAVA 68

Query: 355 ALNGLKMGDKTLTVRRAT 372
             +G  +  + L +  A 
Sbjct: 69  GEDGRMIAGQVLDINLAA 86

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 16/83 (19%)

Query: 175 RRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVE 233
            RV++G L   +  +  +   FS+          G    +V   ++    FAFV+     
Sbjct: 16  SRVFIGNLNTLVVKKSDVEAIFSKY---------GK---IVGCSVHK--GFAFVQYVNER 61

Query: 234 EASNAM-ALDGIIFEGVAVRVRR 255
            A  A+   DG +  G  + +  
Sbjct: 62  NARAAVAGEDGRMIAGQVLDINL 84

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 17/93 (18%), Positives = 28/93 (30%), Gaps = 11/93 (11%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   + V  LP      ++ +LL+ +         K      +K   F    +    
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQA 53

Query: 350 DIACAALNGLKMGDKTLTVRRAT----ASSGQS 378
             A    +      K L V+         SG S
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (126), Expect = 1e-09
 Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 6/76 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V  L    +E  I++   +                  + Y F  + +      A  A
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKP------GAVERVKKIRDYAFVHFSNREDAVEAMKA 63

Query: 356 LNGLKMGDKTLTVRRA 371
           LNG  +    + V  A
Sbjct: 64  LNGKVLDGSPIEVTLA 79

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 1e-08
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 13/82 (15%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           + +YV  L    +E+ I   F+ +                   +   + +AFV     E+
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKP------------GAVERVKKIRDYAFVHFSNRED 56

Query: 235 ASNAM-ALDGIIFEGVAVRVRR 255
           A  AM AL+G + +G  + V  
Sbjct: 57  AVEAMKALNGKVLDGSPIEVTL 78

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.5 bits (125), Expect = 2e-09
 Identities = 34/87 (39%), Positives = 46/87 (52%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VFVG +PY  TE Q+K++    G +  F LV DR+TG  KGYGFC YQD      A   
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQ 382
           LNG +   + L V  A +   + + + 
Sbjct: 70  LNGREFSGRALRVDNAASEKNKEELKS 96

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 8e-06
 Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 8/103 (7%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
           R  R V+VG +P  A E+ +   FS+V   +          V +      K + F E + 
Sbjct: 6   RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRL------VYDRETGKPKGYGFCEYQD 59

Query: 232 VEEASNAM-ALDGIIFEGVAVRVRR-PTDYNPTLAAALGPGQP 272
            E A +AM  L+G  F G A+RV    ++ N     +LG G P
Sbjct: 60  QETALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGTGAP 102

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 2e-09
 Identities = 15/90 (16%), Positives = 31/90 (34%), Gaps = 7/90 (7%)

Query: 290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVT 349
           G+ G   VFVG      TE +++E    +G      ++        + + F  + D  + 
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGD-----VMDVFIPKPFRAFAFVTFADDQIA 55

Query: 350 DIACAALNGLKMGDKTLTVRRATASSGQSK 379
              C     L +   ++ +  A      + 
Sbjct: 56  QSLCG--EDLIIKGISVHISNAEPKHNSNS 83

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.9 bits (98), Expect = 8e-06
 Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 12/81 (14%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+VG       E  +  FFSQ            GD +        + FAFV     + 
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQY-----------GDVMDVFIPKPFRAFAFVTFADDQI 54

Query: 235 ASNAMALDGIIFEGVAVRVRR 255
           A +    + +I +G++V +  
Sbjct: 55  AQSLCG-EDLIIKGISVHISN 74

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.7 bits (123), Expect = 3e-09
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 7/85 (8%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
           R VY+ G P  A    I  +       +          +        K   FV   ++E 
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-------MRRTLHKAFKGSIFVVFDSIES 59

Query: 235 ASNAMALDGIIFEGVAVRVRRPTDY 259
           A   +   G  ++   + +    DY
Sbjct: 60  AKKFVETPGQKYKETDLLILFKDDY 84

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 6e-08
 Identities = 17/76 (22%), Positives = 25/76 (32%), Gaps = 2/76 (2%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            V++ G P   T   IKE LE  G +     ++       KG  F V+            
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFV-E 65

Query: 356 LNGLKMGDKTLTVRRA 371
             G K  +  L +   
Sbjct: 66  TPGQKYKETDLLILFK 81

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.1 bits (122), Expect = 3e-09
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 14/83 (16%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V V G P  +    +  F                   +   +++   +  +  ++  +A 
Sbjct: 7   VTVFGFPQASASYILLQFAQYGNI-------------LKHVMSNTGNWMHIRYQSKLQAR 53

Query: 237 NAMALDGIIFEG-VAVRVRRPTD 258
            A++ DG IF   + + V+   D
Sbjct: 54  KALSKDGRIFGESIMIGVKPCID 76

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 13/77 (16%), Positives = 23/77 (29%), Gaps = 9/77 (11%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V G P          +L  F     +  +      N+  +    YQ       A  + 
Sbjct: 7   VTVFGFPQASAS----YILLQF---AQYGNILKHVMSNTGNWMHIRYQSKLQARKAL-SK 58

Query: 357 NGLKMGDKT-LTVRRAT 372
           +G   G+   + V+   
Sbjct: 59  DGRIFGESIMIGVKPCI 75

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.5 bits (117), Expect = 1e-08
 Identities = 9/76 (11%), Positives = 22/76 (28%), Gaps = 3/76 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V V  LP  + + ++ +  +  G +   D+        +  +    +             
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALA-AITK 59

Query: 357 NGLKMGDKTLTVRRAT 372
               +G   + V   T
Sbjct: 60  THKVVGQNEIIVSHLT 75

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.7 bits (102), Expect = 1e-06
 Identities = 15/81 (18%), Positives = 25/81 (30%), Gaps = 8/81 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V V  LP   N+  +  +F      I           V   +    +FA +E    + A 
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPII--------HVDVADSLKKNFRFARIEFARYDGAL 54

Query: 237 NAMALDGIIFEGVAVRVRRPT 257
            A+     +     + V   T
Sbjct: 55  AAITKTHKVVGQNEIIVSHLT 75

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.8 bits (118), Expect = 2e-08
 Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 1/76 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
             +  +P+  T+  + + LE          V   + G   G     +++      +   L
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RL 69

Query: 357 NGLKMGDKTLTVRRAT 372
           +  K+  +   V   T
Sbjct: 70  HRKKLNGREAFVHVVT 85

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 0.001
 Identities = 10/84 (11%), Positives = 22/84 (26%), Gaps = 6/84 (7%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
              ++  +P    +  +  F   +              V+          A V+ +  ++
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDE------NAVHVLVDNNGQGLGQALVQFKNEDD 62

Query: 235 ASNAMALDGIIFEGVAVRVRRPTD 258
           A  +  L      G    V   T 
Sbjct: 63  ARKSERLHRKKLNGREAFVHVVTL 86

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 296 RVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVT 349
            VFV GL     + ++    E    FG +H   +        S       +  Y      
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 350 DIACAALNGLKMGDKTLTV 368
             A   +N + +  +TL  
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 88

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 2e-08
 Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 6/99 (6%)

Query: 288 IGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPA 347
           + G     R+ V  L Y  T   + ++   FGT+             ++      Y DP 
Sbjct: 1   MAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 56

Query: 348 VTDIACAALNG--LKMGDKTLTVRRATASSGQSKTEQES 384
               A  +L+G  +     TL +  +  +S   K   + 
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDK 95

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (80), Expect = 0.003
 Identities = 16/92 (17%), Positives = 29/92 (31%), Gaps = 17/92 (18%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKK-FAFVEMRTVE 233
            R+ V  L        +   FS+            G  +  +      +  A ++     
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSK-----------FGTVLKIITFTKNNQFQALLQYADPV 56

Query: 234 EASNAM-ALDG--IIFEGVAVRVR--RPTDYN 260
            A +A  +LDG  I      +R+   + T  N
Sbjct: 57  SAQHAKLSLDGQNIYNACCTLRIDFSKLTSLN 88

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 50.7 bits (120), Expect = 2e-08
 Identities = 26/81 (32%), Positives = 41/81 (50%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           +    + V  +P    E Q+++L E +G +    +V DR+T  S+GYGF  +Q  +    
Sbjct: 40  DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A A LNG  + +K L V  A 
Sbjct: 100 AIAGLNGFNILNKRLKVALAA 120

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 38.7 bits (89), Expect = 3e-04
 Identities = 27/143 (18%), Positives = 49/143 (34%), Gaps = 17/143 (11%)

Query: 138 SAVPEMAQNMLPFGAT------QLGAFPLMPVQVMTQQATRHARRVYVGGLPPLANEQAI 191
           S +P ++Q   P+G T      Q      +P   M        R + V  +P   +E  +
Sbjct: 2   SQIPLVSQYD-PYGQTAQLQQLQQQQQQHIPPTQM-NPEPDVLRNLMVNYIPTTVDEVQL 59

Query: 192 ATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA 250
              F +               V +      + + FV+ ++   A  A+  L+G       
Sbjct: 60  RQLFERYGPIE------SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113

Query: 251 VRVR--RPTDYNPTLAAALGPGQ 271
           ++V         P +A A+G G 
Sbjct: 114 LKVALAASGHQRPGIAGAVGDGN 136

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.6 bits (112), Expect = 5e-08
 Identities = 12/79 (15%), Positives = 29/79 (36%), Gaps = 7/79 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + + GLP   T  ++ +LL  +   +             KG  F    +    + A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKY-------CFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 357 NGLKMGDKTLTVRRATASS 375
           +  ++ ++ L+V+     +
Sbjct: 54  HQSRLRERELSVQLQPTDA 72

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.9 bits (113), Expect = 7e-08
 Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            VF+  L +   E  + E+L+ FG L    +V   DT +SKG  F  +          AA
Sbjct: 10  TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 69

Query: 356 LN------GLKMGDKTLTVRRAT 372
            +      GLK+  + L V  A 
Sbjct: 70  ASLEAEGGGLKLDGRQLKVDLAV 92

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.3 bits (83), Expect = 8e-04
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 13/92 (14%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMR 230
               + V++  L   + E+A+     Q               V++    H K  AF +  
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFM 58

Query: 231 TVEEASNAMA-------LDGIIFEGVAVRVRR 255
           T E A   +A         G+  +G  ++V  
Sbjct: 59  TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 90

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.4 bits (112), Expect = 8e-08
 Identities = 12/86 (13%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 171 TRHARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           T   R + +  L   L +E  +   F    +    N             +     AF+  
Sbjct: 1   TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK-----EHSFNNCCAFMVF 55

Query: 230 RTVEEASNAMALDGIIFEGVAVRVRR 255
              + A  A+ ++  +     + V  
Sbjct: 56  ENKDSAERALQMNRSLLGNREISVSL 81

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.5 bits (107), Expect = 4e-07
 Identities = 8/79 (10%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 296 RVFVGGLPYYFTETQIKELL--ESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIAC 353
            + +  L     +  +                    ++   +    F V+++    + A 
Sbjct: 6   EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 354 AALNGLKMGDKTLTVRRAT 372
             +N   +G++ ++V  A 
Sbjct: 66  -QMNRSLLGNREISVSLAD 83

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 1e-07
 Identities = 16/70 (22%), Positives = 31/70 (44%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +++ GL    T+  + +L + +G +     + D+ T   KGYGF  +  P+    A  AL
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 357 NGLKMGDKTL 366
               +  +  
Sbjct: 61  KASGVQAQMA 70

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 7/77 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           +Y+ GL P   +Q +          +   +      +++   N  K + FV+  +   A 
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKA------ILDKTTNKCKGYGFVDFDSPSAAQ 54

Query: 237 NAM-ALDGIIFEGVAVR 252
            A+ AL     +    +
Sbjct: 55  KAVTALKASGVQAQMAK 71

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 1e-07
 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 1/85 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +  A G       V +      F E    E+ E +G +   ++  +    +  G  +  +
Sbjct: 17  SQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKF 75

Query: 344 QDPAVTDIACAALNGLKMGDKTLTV 368
           +     + A   LN      + +  
Sbjct: 76  RREEDAEKAVIDLNNRWFNGQPIHA 100

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (107), Expect = 6e-07
 Identities = 12/89 (13%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 284 ASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVY 343
           +SG          V + GLP+  ++ +I +       +     +     G S G  F  +
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 344 QDPAVTDIACAALNGLKMGDKTLTVRRAT 372
               + +      +  ++G + + + +++
Sbjct: 65  ASQEIAE-KALKKHKERIGHRYIEIFKSS 92

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 7e-07
 Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 293 GPDRVFVGGL-PYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           G   + V  L P   T   +  L   +G +    ++ ++              D     +
Sbjct: 1   GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQL 55

Query: 352 ACAALNGLKMGDKTLTVRRATASSGQSKTEQES 384
           A + LNG K+  K + +  +   + Q   E + 
Sbjct: 56  AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQE 88

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 8e-07
 Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 8/77 (10%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            ++V G     T T ++     FG +       D      +   F  Y+     D A A 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNII------DLSMDPPRNCAFVTYEKMESADQAVAE 58

Query: 356 LNGLKMGDKTLTVRRAT 372
           LNG ++    L V  A 
Sbjct: 59  LNGTQVESVQLKVNIAR 75

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 19/92 (20%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
           A R    +YV G         +   FS                ++++ ++  +  AFV  
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPF------------GNIIDLSMDPPRNCAFVTY 46

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRV----RRP 256
             +E A  A+  L+G   E V ++V    ++P
Sbjct: 47  EKMESADQAVAELNGTQVESVQLKVNIARKQP 78

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 8e-07
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 1/80 (1%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
           + P  +++  LP    E +++ +L+ FG       +    +G S+G GF   +     + 
Sbjct: 16  QDPTNLYISNLPLSMDEQELENMLKPFGQ-VISTRILRDSSGTSRGVGFARMESTEKCEA 74

Query: 352 ACAALNGLKMGDKTLTVRRA 371
                NG  +          
Sbjct: 75  VIGHFNGKFIKTPPGVSAPT 94

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 12/90 (13%), Positives = 26/90 (28%), Gaps = 8/90 (8%)

Query: 166 MTQQATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFA 225
           M +Q  +    +Y+  LP   +EQ +          I          ++       +   
Sbjct: 10  MAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVG 62

Query: 226 FVEMRTVEEASNAM-ALDGIIFEGVAVRVR 254
           F  M + E+    +   +G   +       
Sbjct: 63  FARMESTEKCEAVIGHFNGKFIKTPPGVSA 92

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.2 bits (103), Expect = 1e-06
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 2/81 (2%)

Query: 292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDI 351
             P  +F+G L    +  ++K  +      +   +V  R TG ++ +G+  ++     + 
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 352 ACAALNGLKMGDKTLTVRRAT 372
           A   L GLK+    + + +  
Sbjct: 70  AL-ELTGLKVFGNEIKLEKPK 89

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 20/92 (21%), Positives = 30/92 (32%), Gaps = 13/92 (14%)

Query: 286 GAIGGAEGPD------RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYG 339
           G+ G + GP       RV V GLP   +   +K+ +   G +   D+ KD         G
Sbjct: 1   GSSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MG 53

Query: 340 FCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
              Y      + A   L+  K           
Sbjct: 54  MVEYLRKEDMEYALRKLDDTKFRSHEGETSYI 85

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 23/87 (26%), Gaps = 14/87 (16%)

Query: 170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEM 229
             R   RV V GLPP  + Q +     +                V      +     VE 
Sbjct: 11  TRRSDFRVLVSGLPPSGSWQDLKDHMREAGD-------------VCYADVQKDGMGMVEY 57

Query: 230 RTVEEASNAM-ALDGIIFEGVAVRVRR 255
              E+   A+  LD   F         
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETSY 84

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 4e-06
 Identities = 13/83 (15%), Positives = 23/83 (27%), Gaps = 3/83 (3%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V + GLPY  TE  I               ++    G   G     +        A  A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AK 74

Query: 357 NGLKMGDKTLTVRRATASSGQSK 379
           +   M  + + +   + +     
Sbjct: 75  DKANMQHRYVELFLNSTAGTSGS 97

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 7e-05
 Identities = 21/81 (25%), Positives = 29/81 (35%), Gaps = 8/81 (9%)

Query: 177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEAS 236
           V++ GLP  A E  I  FFS +              +           A VE  T E+A 
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLNP--------MRVHIEIGPDGRVTGEADVEFATHEDAV 69

Query: 237 NAMALDGIIFEGVAVRVRRPT 257
            AMA D    +   V +   +
Sbjct: 70  AAMAKDKANMQHRYVELFLNS 90

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 5e-06
 Identities = 15/106 (14%), Positives = 27/106 (25%), Gaps = 5/106 (4%)

Query: 286 GAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQD 345
           G++    G    F G L        +  L  + G +   D V+    G          + 
Sbjct: 3   GSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL-----FKEK 57

Query: 346 PAVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQESILAQAQQ 391
                      N   +  +   V          K   + I+   Q+
Sbjct: 58  AKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQE 103

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.0 bits (98), Expect = 9e-06
 Identities = 24/99 (24%), Positives = 41/99 (41%), Gaps = 12/99 (12%)

Query: 284 ASGAIGGAEGPD--RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFC 341
           +SG IG  +     R++VGGL    +   +    + FG++   D VK         + + 
Sbjct: 5   SSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYI 58

Query: 342 VYQDPAVTDIACAALNGLKMGDKTLTVR----RATASSG 376
            Y+       ACA + G  +G     +R    ++  SSG
Sbjct: 59  QYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSSG 97

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (94), Expect = 3e-05
 Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 13/81 (16%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
            R++VGGL P  +  A+A  F +              ++  +       FA+++  +++ 
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRF------------GSIRTIDHVKGDSFAYIQYESLDA 65

Query: 235 ASNAM-ALDGIIFEGVAVRVR 254
           A  A   + G    G   R+R
Sbjct: 66  AQAACAKMRGFPLGGPDRRLR 86

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.9 bits (92), Expect = 6e-05
 Identities = 16/99 (16%), Positives = 27/99 (27%), Gaps = 10/99 (10%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           +    LP      +I+E      T   F  +               + +P     A   L
Sbjct: 13  ILAKNLPAGTLAAEIQE------TFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHL 66

Query: 357 NGLKMGDKTLTVRRAT----ASSGQSKTEQESILAQAQQ 391
              K     L +  A      ++ Q K  Q    A+  +
Sbjct: 67  AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 15/87 (17%)

Query: 169 QATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVE 228
            AT+    V  GGL    +   +     +               V  + +   K ++F  
Sbjct: 16  YATQS-LVVANGGLGNGVSRNQLLPVLEKC------------GLVDALLMPPNKPYSFAR 62

Query: 229 MRTVEEASNAM-ALDG-IIFEGVAVRV 253
            RT EE+  A   L+G  + + +  ++
Sbjct: 63  YRTTEESKRAYVTLNGKEVVDDLGQKI 89

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 1e-04
 Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V  GGL    +  Q+  +LE  G +    +  ++       Y F  Y+    +  A   L
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 357 NGLKMGDK 364
           NG ++ D 
Sbjct: 77  NGKEVVDD 84

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 2e-04
 Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 5/76 (6%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           + +  +P   +E  +K L  S G +        +D    +               A   L
Sbjct: 13  LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEEAVQALIDL 68

Query: 357 NGLKMGD-KTLTVRRA 371
           +   +G+   L V  +
Sbjct: 69  HNHDLGENHHLRVSFS 84

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 19/95 (20%), Positives = 32/95 (33%), Gaps = 7/95 (7%)

Query: 171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI--NHEKKFAFVE 228
            RH R V +  +    + +      +++   +          +  + +   H    A V 
Sbjct: 5   MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLR-VECSKFGQIRKLLLFDRHPDGVASVS 63

Query: 229 MRTVEEASNAM-ALDGIIFEGVAVRV---RRPTDY 259
            R  EEA   +  LDG  F G  +        TDY
Sbjct: 64  FRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 1/59 (1%)

Query: 313 ELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA 371
           +L            +      +  G     ++DP   D     L+G   G + +T +  
Sbjct: 35  DLRVECSKFGQIRKLL-LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 92

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 2e-04
 Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL 356
           V++ GLP+      + +  +    +     +     G + G GF  +++ A    A    
Sbjct: 21  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK-AALCR 79

Query: 357 NGLKMGDKTLTVRRATASSGQSKTEQ 382
           +   MG++ + V   T      K + 
Sbjct: 80  HKQYMGNRFIQVHPITKKGMLEKIDM 105

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.6 bits (81), Expect = 0.002
 Identities = 15/86 (17%), Positives = 25/86 (29%), Gaps = 6/86 (6%)

Query: 172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRT 231
                VY+ GLP  A  + +  FF ++              +            FVE R 
Sbjct: 16  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVE------DSIYIAYGPNGKATGEGFVEFRN 69

Query: 232 VEEASNAMALDGIIFEGVAVRVRRPT 257
             +   A+           ++V   T
Sbjct: 70  EADYKAALCRHKQYMGNRFIQVHPIT 95

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.5 bits (86), Expect = 4e-04
 Identities = 16/104 (15%), Positives = 29/104 (27%), Gaps = 11/104 (10%)

Query: 284 ASGAIGGAEGPD---RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGF 340
           +SG+ G          V V GL     E  + E       L  F  +        K    
Sbjct: 2   SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEA------LEKFGTICYVMMMPFKRQAL 55

Query: 341 CVYQDP--AVTDIACAALNGLKMGDKTLTVRRATASSGQSKTEQ 382
             +++   A   +  AA   + +  +      +T+         
Sbjct: 56  VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNS 99

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.5 bits (81), Expect = 0.002
 Identities = 16/99 (16%), Positives = 27/99 (27%), Gaps = 23/99 (23%)

Query: 175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEE 234
             V+V GL     E  +     +               +  V +   K+ A VE   ++ 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKF------------GTICYVMMMPFKRQALVEFENIDS 63

Query: 235 ASNA---MALDGIIFEGVAVRV--------RRPTDYNPT 262
           A       A   +   G              RP +  P+
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPS 102

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 14/89 (15%), Positives = 25/89 (28%), Gaps = 7/89 (7%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
           RV V GLP   +   +K+ +   G +   D+ +D         G   +        A   
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 356 LNGLKMGDKTLTVRRATASSGQSKTEQES 384
           L+  K                  ++    
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYG 83

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.2 bits (80), Expect = 0.002
 Identities = 11/77 (14%), Positives = 33/77 (42%), Gaps = 4/77 (5%)

Query: 296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAA 355
            + +  LP   TET++  L   FG +    ++K ++      +     ++ A+T +   +
Sbjct: 10  VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ----AFLELATEEAAITMVNYYS 65

Query: 356 LNGLKMGDKTLTVRRAT 372
                + ++ + ++ + 
Sbjct: 66  AVTPHLRNQPIYIQYSN 82

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	435
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.97
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.86
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.86
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.85
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.85
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.84
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.84
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.83
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.83
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.82
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.81
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.81
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.81
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.79
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.78
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.78
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.77
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.77
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.77
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.77
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.77
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.76
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.76
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.75
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.75
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.74
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.74
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.74
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.73
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.72
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.72
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.72
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.71
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.69
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.69
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.67
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.67
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.67
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.67
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.67
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.67
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.66
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.66
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.66
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.65
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.65
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.65
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.65
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.65
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.65
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.64
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.64
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.64
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.64
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.64
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.64
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.64
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.63
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.63
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.63
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.63
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.63
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.63
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.63
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.63
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.62
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.62
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.62
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.62
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.61
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.6
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.6
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.59
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.59
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.59
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.59
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.59
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.58
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.58
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.58
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.56
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.56
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.56
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.56
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.55
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.55
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.54
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.54
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.53
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.53
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.52
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.52
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.49
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.47
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.47
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.45
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.45
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.38
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.35
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	U2	99.11
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.11
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.84
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	98.18
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.85
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.84
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.98
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.33
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.1
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.75
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	87.56

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.1e-31  Score=229.70  Aligned_cols=171  Identities=22%  Similarity=0.398  Sum_probs=143.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..++|||+|||+.+|+++|+++|++||.|..+.      .+.+..++.++|||||+|.+.++|..|+.+++..+.++.+.
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~------~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~   78 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   78 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEE------eeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchh
Confidence            347999999999999999999999999864311      11222345678999999999999999999899999999988


Q ss_pred             EcCCCCCCcchhhcCCCCCCCCCccccccccccCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCC
Q 013837          253 VRRPTDYNPTLAAALGPGQPSPNLNLAAVGLASGAIGGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDT  332 (435)
Q Consensus       253 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~t  332 (435)
                      +.+........                       ........++|||+|||..+|+++|+++|+.||.|..+.|+.+..+
T Consensus        79 ~~~~~~~~~~~-----------------------~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~  135 (183)
T d1u1qa_          79 PKRAVSREDSQ-----------------------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS  135 (183)
T ss_dssp             EEECCCTTGGG-----------------------STTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTT
T ss_pred             hhhhhhccccc-----------------------ccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeeccccc
Confidence            87654433211                       1122344578999999999999999999999999999999999889


Q ss_pred             CCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          333 GNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       333 g~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      |.++|||||+|.+.++|.+||+ +++..|.|+.|.|.+|.+
T Consensus       136 ~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         136 GKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             CCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEECCC
T ss_pred             CccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEecCC
Confidence            9999999999999999999997 799999999999999854

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.87  E-value=3.4e-22  Score=147.11  Aligned_cols=81  Identities=26%  Similarity=0.439  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999975


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      .
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.8e-22  Score=149.61  Aligned_cols=84  Identities=30%  Similarity=0.453  Sum_probs=79.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            7764

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.86  E-value=7.8e-22  Score=146.90  Aligned_cols=82  Identities=28%  Similarity=0.342  Sum_probs=78.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ...+|||+|||..+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|.|+.|+|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=6.6e-22  Score=148.05  Aligned_cols=83  Identities=29%  Similarity=0.434  Sum_probs=79.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|+|+.|+|.||
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      +++
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            765

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.5e-21  Score=143.71  Aligned_cols=79  Identities=37%  Similarity=0.606  Sum_probs=76.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ++|||+|||..+|+++|+++|++||.|..|.|+.+..+|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.||+|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5799999999999999999999999999999999988999999999999999999999999999999999999999965

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=5.4e-22  Score=148.21  Aligned_cols=83  Identities=18%  Similarity=0.323  Sum_probs=78.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.||.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.2e-21  Score=143.24  Aligned_cols=77  Identities=23%  Similarity=0.327  Sum_probs=75.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .|||+|||+.+|+++|.++|+.||.|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|.|+.|+|.||+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            59999999999999999999999999999999999999999999999999999999999999999999999999994

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.4e-21  Score=148.36  Aligned_cols=84  Identities=25%  Similarity=0.485  Sum_probs=79.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||+.+|+++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..||+.|||..|.|+.|+|.||
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      .++.
T Consensus        96 ~~k~   99 (102)
T d2cpza1          96 RSKN   99 (102)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7764

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.6e-21  Score=144.76  Aligned_cols=83  Identities=24%  Similarity=0.383  Sum_probs=78.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|..||+.|||..|.|+.|+|.||
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      ...
T Consensus        85 ~~~   87 (93)
T d1h2vz_          85 AGF   87 (93)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.85  E-value=2.3e-21  Score=147.90  Aligned_cols=84  Identities=26%  Similarity=0.440  Sum_probs=79.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.+|
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8764

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.2e-21  Score=143.00  Aligned_cols=78  Identities=22%  Similarity=0.437  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      +.+.++|||+|||..+|+++|+++|++||.|.+|.|+.++.+|.++|||||+|.+.++|.+||..|||..|+|+.|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345678999999999999999999999999999999999999999999999999999999999999999999999987

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.1e-21  Score=145.00  Aligned_cols=81  Identities=56%  Similarity=0.965  Sum_probs=77.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      .+|||+|||..+|+++|+++|++||.|..|.|++++.||.++|||||+|.++++|..|++.|||..|.|+.|.|.||+..
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999765


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=6.7e-21  Score=141.90  Aligned_cols=83  Identities=23%  Similarity=0.388  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.  +..|+|+.|.|.+|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            4457899999999999999999999999999999999999999999999999999999999984  45899999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        84 ~~k~~   88 (90)
T d2cqga1          84 NSKQS   88 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            87653

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.84  E-value=6e-21  Score=141.17  Aligned_cols=79  Identities=25%  Similarity=0.458  Sum_probs=75.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRR  370 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~  370 (435)
                      ..++|||+|||..+|+++|+++|++||.|..+.|++++.+|.++|||||+|.+.++|.+||+.|||..+.|  ++|+|.|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            34679999999999999999999999999999999999999999999999999999999999999999976  8899999


Q ss_pred             c
Q 013837          371 A  371 (435)
Q Consensus       371 a  371 (435)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            7

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=7e-21  Score=143.44  Aligned_cols=84  Identities=24%  Similarity=0.459  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCC-CCCcceEEEEEEcCHHHHHHHHHHh-CCceeCCeEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRD-TGNSKGYGFCVYQDPAVTDIACAAL-NGLKMGDKTLTVR  369 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~-tg~~~G~afV~f~~~~~A~~Al~~l-~g~~~~g~~l~V~  369 (435)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+.. +|.++|||||+|.+.++|.+||+.| ||..|.|+.|.|.
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3456899999999999999999999999999999988754 7999999999999999999999998 8999999999999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      ||....
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997764

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=7.9e-21  Score=140.36  Aligned_cols=78  Identities=28%  Similarity=0.500  Sum_probs=74.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEEEc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVRRA  371 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~~a  371 (435)
                      .++|||+|||..+|+++|+++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|.||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            3679999999999999999999999999999999999899999999999999999999999999999987  55999987

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1e-20  Score=139.22  Aligned_cols=79  Identities=27%  Similarity=0.518  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|+.||.|..+.|+.++.+|.++|||||+|.+.++|.+||+ ++|..|.|+.|+|..|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            34689999999999999999999999999999999999999999999999999999999998 69999999999999884

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.9e-20  Score=139.97  Aligned_cols=83  Identities=27%  Similarity=0.403  Sum_probs=76.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..|.|+.+..+  .+|||||+|.+.++|..|++.|||..|.|+.|+|.||
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44579999999999999999999999999999999998654  3799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      +++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.84  E-value=8.7e-21  Score=137.67  Aligned_cols=76  Identities=25%  Similarity=0.413  Sum_probs=73.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +|||+|||+.+|+++|+++|++||.|..+.|+.++ +|.++|||||+|.+.++|.+|++.|||..|.|+.|+|.+|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999986 79999999999999999999999999999999999999985

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.84  E-value=2.4e-20  Score=151.72  Aligned_cols=85  Identities=31%  Similarity=0.531  Sum_probs=80.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|+.||.|++|.|+.++.||.++|||||+|.+.++|..||+.|||..|+|+.|+|.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34457899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      |..+.
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            97654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=5.3e-21  Score=140.24  Aligned_cols=79  Identities=16%  Similarity=0.257  Sum_probs=69.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ++|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|++.|||..|.|+.|.|.||+|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5899999999999999999999999999888888878899999999999999999999999999999999999999965

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7.7e-21  Score=142.35  Aligned_cols=83  Identities=29%  Similarity=0.569  Sum_probs=78.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ..+|||+|||+.+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.++++|..||+.|||..|+|+.|+|.+|.+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~   84 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGK   84 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEEC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999977


Q ss_pred             CCC
Q 013837          374 SSG  376 (435)
Q Consensus       374 ~~~  376 (435)
                      +..
T Consensus        85 ~~~   87 (90)
T d1x5sa1          85 SSD   87 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.7e-20  Score=139.93  Aligned_cols=85  Identities=25%  Similarity=0.559  Sum_probs=77.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      ......++|||+|||+.+|+++|+++|+.||.|..|.|+.++  +.++|||||+|.+.++|.+||..|||..|.|+.|+|
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   83 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   83 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            334556789999999999999999999999999999999885  347999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .||+++.
T Consensus        84 ~~A~~r~   90 (93)
T d2cq3a1          84 NNATARV   90 (93)
T ss_dssp             EECCSSC
T ss_pred             EecCcCC
Confidence            9998764

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=8.9e-21  Score=139.69  Aligned_cols=79  Identities=30%  Similarity=0.515  Sum_probs=74.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeE-EEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHG-FDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~-v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      |||+|||..+|+++|+++|++||.|.. +.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999866 4788898899999999999999999999999999999999999999998764

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=9.2e-21  Score=145.99  Aligned_cols=81  Identities=42%  Similarity=0.727  Sum_probs=77.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            35899999999999999999999999999999999999999999999999999999999999999999999999999965


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      +
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=3.2e-21  Score=139.29  Aligned_cols=76  Identities=28%  Similarity=0.496  Sum_probs=73.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ++|||+|||+.+|+++|+++|++||.|..+.|+.++.||.++|||||+|.+.++|.+||+ +|++.|+|+.|.|.+|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999998 7999999999999987

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.7e-20  Score=142.70  Aligned_cols=81  Identities=33%  Similarity=0.630  Sum_probs=76.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||+.+|+++|+++|++||.|.+|.|+.++.||.++|||||+|.+.++|.+||+.+|+ .|.|+.|.|.+|..
T Consensus        10 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~~   88 (103)
T d2cqda1          10 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAYL   88 (103)
T ss_dssp             SSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEESTT
T ss_pred             CcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcCC
Confidence            46799999999999999999999999999999999999999999999999999999999998876 79999999999976


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      +.
T Consensus        89 ~~   90 (103)
T d2cqda1          89 GA   90 (103)
T ss_dssp             TC
T ss_pred             CC
Confidence            53

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.82  E-value=2.1e-20  Score=138.36  Aligned_cols=78  Identities=24%  Similarity=0.479  Sum_probs=73.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCC---CcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTG---NSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg---~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      |||+|||..+|+++|+++|++||.|..|.|+.++.++   .++|||||+|.+.++|.+|++.|||..|+|+.|.|.||..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999987665   4789999999999999999999999999999999999964


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=1.4e-20  Score=143.42  Aligned_cols=78  Identities=17%  Similarity=0.359  Sum_probs=74.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||+|||+.+|+++|+++|+.||.|..|.|+.++.+|.++|||||+|.+.++|.+||. |||..|.|+.|.|.+|.
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            3689999999999999999999999999999999999999999999999999999999996 99999999999999984

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=2.6e-20  Score=142.36  Aligned_cols=81  Identities=26%  Similarity=0.497  Sum_probs=76.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||+.+|+++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.+|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3689999999999999999999999999999999999999999999999999999999997 799999999999999987


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      +.
T Consensus        99 ke  100 (103)
T d1x4ba1          99 RE  100 (103)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.6e-20  Score=135.11  Aligned_cols=75  Identities=28%  Similarity=0.570  Sum_probs=71.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +|||+|||+.+|+++|.++|++||.|..+.|+.++.+|.++|||||+|.+.++|.+||+ +++..|.|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 7999999999999764

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.1e-20  Score=135.47  Aligned_cols=75  Identities=23%  Similarity=0.432  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+||+ ++++.|+|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            59999999999999999999999999999999999999999999999999999999998 5888999999999875

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.81  E-value=2.5e-20  Score=137.92  Aligned_cols=81  Identities=16%  Similarity=0.357  Sum_probs=70.9

Q ss_pred             CCeEEEcCCCCCCC-HHHHHHHHHhcCCeeEEEEeec-CCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          294 PDRVFVGGLPYYFT-ETQIKELLESFGTLHGFDLVKD-RDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       294 ~~~l~V~nLp~~~t-e~~l~~~F~~~G~v~~v~i~~~-~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .++|||+|||..+| +++|+++|++||.|+.|.|+.+ ..+|.++|||||+|.+.++|.+||+ |||..|+|+.|+|.+|
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEEC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEEc
Confidence            57999999999976 5569999999999999998764 4689999999999999999999996 9999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ++++
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8763

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.7e-20  Score=144.60  Aligned_cols=79  Identities=20%  Similarity=0.435  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|.++|++||.|+.|.|..+   +.++|||||+|.+.++|..||+.|||..|.|+.|.|.|+.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999999999998764   5679999999999999999999999999999999999986


Q ss_pred             CC
Q 013837          373 AS  374 (435)
Q Consensus       373 ~~  374 (435)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=9.1e-20  Score=132.88  Aligned_cols=77  Identities=22%  Similarity=0.515  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+. |||..|+|+.|.|..|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999996 8999999999999987

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.4e-20  Score=138.24  Aligned_cols=80  Identities=23%  Similarity=0.463  Sum_probs=74.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      ..+|||+|||..+|+++|+++|+.||.|..+.|+.+.  +.++|||||+|.+.++|.+||+.|||..|+|+.|.|.+|.+
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            3579999999999999999999999999999999985  44789999999999999999999999999999999999976


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      +.
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.1e-19  Score=138.40  Aligned_cols=84  Identities=29%  Similarity=0.428  Sum_probs=78.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhC------CceeCCeE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALN------GLKMGDKT  365 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~------g~~~~g~~  365 (435)
                      ...++|||+|||+.+|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+||+.||      |..|.|+.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            445789999999999999999999999999999999998899999999999999999999999886      67899999


Q ss_pred             EEEEEccCCC
Q 013837          366 LTVRRATASS  375 (435)
Q Consensus       366 l~V~~a~~~~  375 (435)
                      |+|.||.++.
T Consensus        86 l~v~~a~~k~   95 (98)
T d1x4ha1          86 LKVDLAVTRD   95 (98)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997764

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.3e-19  Score=138.79  Aligned_cols=85  Identities=21%  Similarity=0.368  Sum_probs=77.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCee--------EEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLH--------GFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD  363 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~--------~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g  363 (435)
                      ...++|||+|||..+|+++|+++|+.||.|.        .+.+..++.+|.++|||||+|.+.++|.+||+.|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4467999999999999999999999999873        56777888889999999999999999999999999999999


Q ss_pred             eEEEEEEccCCCC
Q 013837          364 KTLTVRRATASSG  376 (435)
Q Consensus       364 ~~l~V~~a~~~~~  376 (435)
                      +.|+|.+|++++.
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987643

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=7e-20  Score=132.15  Aligned_cols=75  Identities=25%  Similarity=0.585  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      +|||+|||..+|+++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+||+ |||..|+|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999999899999999999999999999997 9999999999999986

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.1e-19  Score=134.63  Aligned_cols=76  Identities=18%  Similarity=0.393  Sum_probs=71.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||..+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++|.+||..|||..|.|+.|+|.|++.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999999876      68999999999999999999999999999999999977


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ++
T Consensus        92 ~p   93 (96)
T d1x4ga1          92 SP   93 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.9e-20  Score=141.48  Aligned_cols=84  Identities=20%  Similarity=0.265  Sum_probs=79.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .+.++|||+|||..+|+++|+++|+.||.|..+.++.+..+|.++|||||+|.+.++|..||+.|||..|.|+.|+|.||
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45679999999999999999999999999999988888778999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      +++.
T Consensus        96 k~k~   99 (102)
T d2cpxa1          96 KNKK   99 (102)
T ss_dssp             CCCS
T ss_pred             CCcc
Confidence            8764

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7.7e-19  Score=132.51  Aligned_cols=80  Identities=20%  Similarity=0.403  Sum_probs=72.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|.+||+.|||..|.|+.|+|.||
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a   88 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   88 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            44568999999999999999999999999998887654   457899999999999999999999999999999999999


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      +..
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=2.2e-19  Score=133.04  Aligned_cols=80  Identities=16%  Similarity=0.329  Sum_probs=71.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.++++||+++|+.||.|....++.+..+|.++|||||+|.+.++|.+||+.|||..|.|+.|+|.++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999999876433344468999999999999999999999999999999999999985

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.78  E-value=4.9e-20  Score=137.67  Aligned_cols=81  Identities=17%  Similarity=0.331  Sum_probs=73.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.+|+++|+++|+.||.|..+.|+.+ .+|.++|||||+|.+.++|.+||+ |||..|.|+.|+|.+|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEec
Confidence            44568999999999999999999999999998888655 579999999999999999999996 9999999999999999


Q ss_pred             cCC
Q 013837          372 TAS  374 (435)
Q Consensus       372 ~~~  374 (435)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            653

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=6.7e-19  Score=129.66  Aligned_cols=77  Identities=22%  Similarity=0.263  Sum_probs=72.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||+|||..+|+++|.++|+.||.|..|.|..+. +|.++|||||+|.+.++|.+||+ ++|..|.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999998875 79999999999999999999997 79999999999999864

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.78  E-value=4.6e-19  Score=130.18  Aligned_cols=76  Identities=20%  Similarity=0.312  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~V~~  370 (435)
                      .+.++|||+|||..+|+++|.++|+.||.|..|.++++     .+|||||+|.+.++|..|++.|||..| +|+.|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            45679999999999999999999999999999999765     368999999999999999999999998 478999999


Q ss_pred             cc
Q 013837          371 AT  372 (435)
Q Consensus       371 a~  372 (435)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            95

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=4e-19  Score=131.21  Aligned_cols=77  Identities=34%  Similarity=0.556  Sum_probs=71.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+++++|+++|+.||.|..|.+.++      +|||||+|.+.++|.+|++.|||..|.|+.|+|+||.
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~   80 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFAC   80 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            3467999999999999999999999999999999865      5799999999999999999999999999999999998


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      .+.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            765

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7.1e-19  Score=135.30  Aligned_cols=83  Identities=28%  Similarity=0.497  Sum_probs=73.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecC-CCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~-~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .+..+|||+|||+.+|+++|+++|+.|| |+.+.++.+. .+|.++|||||+|.+.++|++|+. |||..|.|+.|+|.+
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            4567999999999999999999999999 6777777765 478899999999999999987775 999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      |.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987653

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.77  E-value=4e-19  Score=132.10  Aligned_cols=77  Identities=19%  Similarity=0.318  Sum_probs=70.4

Q ss_pred             CCCeEEEcCCCCCCCHHHH---HHHHHhcCCeeEEEEeecCCCCCc---ceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          293 GPDRVFVGGLPYYFTETQI---KELLESFGTLHGFDLVKDRDTGNS---KGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l---~~~F~~~G~v~~v~i~~~~~tg~~---~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ..++|||+|||+.+++++|   .++|++||.|..|.|++++.++.+   .|||||+|.+.++|.+||+.|||..|+|+.|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4568999999999999999   678999999999999999776554   4999999999999999999999999999999


Q ss_pred             EEE
Q 013837          367 TVR  369 (435)
Q Consensus       367 ~V~  369 (435)
                      +|+
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            985

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=2.1e-18  Score=127.65  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=70.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ..++|||+|||..+|+++|+++|+.||.|..+.+..      ++|||||+|.+.++|..||..|||..|.|+.|.|.||+
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            347899999999999999999999999998777754      47899999999999999999999999999999999998


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ++.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            664

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.9e-19  Score=129.44  Aligned_cols=75  Identities=19%  Similarity=0.319  Sum_probs=68.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCc-eeCCeEEEEEEccC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGL-KMGDKTLTVRRATA  373 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~-~~~g~~l~V~~a~~  373 (435)
                      ++|||+|||..+|+++|+++|++||.|..+.+...      +|||||+|.+.++|.+|++.|||. .|.|+.|.|.||.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            47999999999999999999999999987777654      689999999999999999999996 69999999999987


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            64

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=7.9e-19  Score=127.49  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=69.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+||+  +|+++|+++|++||.|..|.+.++      +|||||+|.+.++|..|+..|||..|.|+.|+|.||
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345799999996  899999999999999999998764      579999999999999999999999999999999999


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            7664

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=1.3e-18  Score=133.52  Aligned_cols=85  Identities=13%  Similarity=0.229  Sum_probs=76.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .....+|||+|||+.+|+++|+++|..||.|..+.++.+..++.++|||||+|.+.++|.+|++ +|+..|.|+.|.|.+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3445689999999999999999999999998887677776789999999999999999999997 899999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      ++....
T Consensus        91 ~~~~~~   96 (104)
T d1wg5a_          91 SSRAEV   96 (104)
T ss_dssp             ECTTTS
T ss_pred             CCHHHh
Confidence            987654

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=8.9e-19  Score=132.44  Aligned_cols=81  Identities=16%  Similarity=0.327  Sum_probs=72.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....++|||+|||..+|+++|+++|++||.|..+.     .++.++|||||+|.+.++|.+|+..|||..|.|+.|+|.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34467999999999999999999999999876553     2578899999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 013837          371 ATASSG  376 (435)
Q Consensus       371 a~~~~~  376 (435)
                      |.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            987754

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=5.6e-19  Score=134.84  Aligned_cols=81  Identities=19%  Similarity=0.440  Sum_probs=74.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||..+|+++|+++|+.||.|..+.+..+. ++.++|||||+|.+.++|.+||+.|||..|.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345789999999999999999999999999999998884 7899999999999999999999999999999999988776


Q ss_pred             cC
Q 013837          372 TA  373 (435)
Q Consensus       372 ~~  373 (435)
                      .+
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.6e-18  Score=131.06  Aligned_cols=76  Identities=21%  Similarity=0.456  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLP-YYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp-~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      ....+|||+||| ..+++++|+++|++||.|+.|.|        ++|||||+|.+.++|.+||+.|||..|.|+.|+|.|
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            344679999996 57889999999999999999988        368999999999999999999999999999999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      |.++.
T Consensus        85 a~~~~   89 (98)
T d1wf2a_          85 AAEPK   89 (98)
T ss_dssp             TTSCC
T ss_pred             CCCCC
Confidence            97653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.6e-18  Score=134.67  Aligned_cols=77  Identities=17%  Similarity=0.270  Sum_probs=70.7

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          294 PDRVFVGGLPY-YFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       294 ~~~l~V~nLp~-~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .++|||+|||+ .+|+++|+++|+.||.|+.|.|+.++     +|||||+|.++++|.+||+.|||..|.|+.|+|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999954 69999999999999999999998873     7899999999999999999999999999999999997


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.1e-18  Score=128.22  Aligned_cols=78  Identities=13%  Similarity=0.094  Sum_probs=69.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee-CCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM-GDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~-~g~~l~V~~  370 (435)
                      .++++|||+|||..+|+++|+++|+.||.|..+.+...    ..+|||||+|.+.++|.+|+..|||..| .|+.|+|.|
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            34679999999999999999999999999988776554    3578999999999999999999999998 589999999


Q ss_pred             ccC
Q 013837          371 ATA  373 (435)
Q Consensus       371 a~~  373 (435)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            965

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.75  E-value=2.4e-18  Score=123.35  Aligned_cols=74  Identities=12%  Similarity=0.188  Sum_probs=68.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ++|||+|||+.+++++|+++|+.||.|..|.|..++.  ..+|||||+|.+.++|.+||. +||..|+|+.|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999999864  346799999999999999996 8999999999999876

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=9e-19  Score=130.99  Aligned_cols=80  Identities=15%  Similarity=0.372  Sum_probs=71.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEE
Q 013837          293 GPDRVFVGGLPYYFTETQIKE----LLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTV  368 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~----~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V  368 (435)
                      +.++|||+|||..+|++||++    +|++||.|..|.+..   ++.++|||||+|.+.++|.+|++.|||..|.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            357999999999999998864    689999999988765   4668999999999999999999999999999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .||+.+.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997653

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.4e-18  Score=131.40  Aligned_cols=81  Identities=19%  Similarity=0.322  Sum_probs=73.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCC-eeEEEEeecC-CCCCcceEEEEEEcCHHHHHHHHHHhCC--ceeCCeEEEEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGT-LHGFDLVKDR-DTGNSKGYGFCVYQDPAVTDIACAALNG--LKMGDKTLTVRR  370 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~-v~~v~i~~~~-~tg~~~G~afV~f~~~~~A~~Al~~l~g--~~~~g~~l~V~~  370 (435)
                      ++|||+|||..+|+++|+++|+.||. |..|.|+++. .+|.++|||||+|.+.++|..|++.|++  ..++|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            57999999999999999999999996 8999999875 4688999999999999999999999864  566899999999


Q ss_pred             ccCCC
Q 013837          371 ATASS  375 (435)
Q Consensus       371 a~~~~  375 (435)
                      |+++.
T Consensus        82 A~p~~   86 (96)
T d2disa1          82 AEPEI   86 (96)
T ss_dssp             SCSSC
T ss_pred             cCCCC
Confidence            98764

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2.6e-19  Score=127.84  Aligned_cols=71  Identities=23%  Similarity=0.452  Sum_probs=68.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEE
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLT  367 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~  367 (435)
                      |||+|||..+|+++|.++|+.||.|..+.+..++.++.++|||||+|.+.++|.+|++.|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999998764

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=2e-18  Score=131.91  Aligned_cols=84  Identities=15%  Similarity=0.177  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          290 GAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       290 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ......+|||+|||+++|+++|+++|..||. ..|.++.+. +|..+|||||+|.+.++|++||+ ||+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3455679999999999999999999999985 578888875 58999999999999999999997 89999999999999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      +++....
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=1.7e-18  Score=134.94  Aligned_cols=76  Identities=18%  Similarity=0.166  Sum_probs=70.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||+.+|+++|+++|+.||.|..|.|..      .+|||||+|.+.++|.+||+.|||..|.|+.|.|.||..
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~   83 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPI   83 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEET
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCC
Confidence            46899999999999999999999999999988743      478999999999999999999999999999999999976


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ..
T Consensus        84 ~~   85 (111)
T d1whxa_          84 GV   85 (111)
T ss_dssp             TT
T ss_pred             Cc
Confidence            54

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=3.2e-18  Score=126.85  Aligned_cols=76  Identities=16%  Similarity=0.233  Sum_probs=66.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      ...+|||+|||+.+|++||+++|++||. ..+.+      +..+|||||+|.+.++|++||+.|||..|.|+.|.|+|+.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3568999999999999999999999993 33433      2358899999999999999999999999999999999996


Q ss_pred             CCC
Q 013837          373 ASS  375 (435)
Q Consensus       373 ~~~  375 (435)
                      .+.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=3.3e-18  Score=132.26  Aligned_cols=81  Identities=21%  Similarity=0.235  Sum_probs=73.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee--CCeEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM--GDKTLTVR  369 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~--~g~~l~V~  369 (435)
                      .+..+|||+|||+.+|+++|+++|++||.|..|.|+.++    .+|||||+|.+.++|+.||..|||..|  .|+.|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345679999999999999999999999999999998874    489999999999999999999999998  58899999


Q ss_pred             EccCCCC
Q 013837          370 RATASSG  376 (435)
Q Consensus       370 ~a~~~~~  376 (435)
                      |++.+..
T Consensus        81 ~s~~~~~   87 (108)
T d2adba1          81 FSKLTSL   87 (108)
T ss_dssp             ECSSCSC
T ss_pred             ecCCccc
Confidence            9977653

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=1.1e-17  Score=126.60  Aligned_cols=78  Identities=24%  Similarity=0.503  Sum_probs=71.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCC--eEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGD--KTLTVR  369 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g--~~l~V~  369 (435)
                      .+.++|||+|||.++|+++|+++|++||.|..|.+.++      ++||||+|.+.++|.+|++.|||..|.|  +.|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            45689999999999999999999999999999998765      6799999999999999999999999976  589999


Q ss_pred             EccCCC
Q 013837          370 RATASS  375 (435)
Q Consensus       370 ~a~~~~  375 (435)
                      ||+..+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            997654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=6.9e-19  Score=130.37  Aligned_cols=74  Identities=20%  Similarity=0.239  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATAS  374 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~  374 (435)
                      ++|||+|||+.+|+++|+++|++||.|..+.|..+       |||||+|.+.++|.+||..|||..|.|+.|+|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            36999999999999999999999999999988653       79999999999999999999999999999999998654


Q ss_pred             C
Q 013837          375 S  375 (435)
Q Consensus       375 ~  375 (435)
                      .
T Consensus        74 ~   74 (87)
T d3begb1          74 V   74 (87)
T ss_dssp             E
T ss_pred             c
Confidence            3

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.2e-17  Score=124.02  Aligned_cols=79  Identities=14%  Similarity=0.160  Sum_probs=71.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh--CCceeCCeEEEE
Q 013837          291 AEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLTV  368 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~V  368 (435)
                      ..+.++|||+|||..+|+++|.++|++||.|..+.+.++      +|||||+|.+.++|.+|++.+  ++..+.|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            356789999999999999999999999999999988765      579999999999999999865  678999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9997664

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.73  E-value=1e-17  Score=124.83  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=72.4

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....+|||+|||+.+|+++|+++|..||.|..+.       +.+..++.++|||||+|.+.++|.+||++|+..|+|++|
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~-------v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i   83 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-------VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEI   83 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCC-------CCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEE
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEee-------eeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEE
Confidence            4567899999999999999999999999998753       446678999999999999999999999999999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        84 ~V~~ak~   90 (91)
T d1fjeb1          84 KLEKPKG   90 (91)
T ss_dssp             EEECCCC
T ss_pred             EEEecCC
Confidence            9998753

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=3e-18  Score=131.41  Aligned_cols=80  Identities=14%  Similarity=0.182  Sum_probs=71.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....||||+|||+.+|+++|.++|..||.|..+.++....+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|.++
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVV   84 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEEC
Confidence            345689999999999999999999999998775555555689999999999999999999996 9999999999999998


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=1.8e-17  Score=127.09  Aligned_cols=81  Identities=16%  Similarity=0.124  Sum_probs=72.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh--CCceeCCeEE
Q 013837          289 GGAEGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTL  366 (435)
Q Consensus       289 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l--~g~~~~g~~l  366 (435)
                      ....+..+|||+|||..+|+++|.++|++||.|..|.+.++      +|+|||+|.+.++|+.||..|  ++..++|+.|
T Consensus        10 ~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l   83 (104)
T d1wexa_          10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEE
Confidence            34466789999999999999999999999999999988764      679999999999999999977  5678899999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|.|++.+.
T Consensus        84 ~v~~s~~~~   92 (104)
T d1wexa_          84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEcCCCc
Confidence            999997654

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.5e-18  Score=127.59  Aligned_cols=78  Identities=19%  Similarity=0.423  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ...++|||+|||+.+|+++|+++|++||.|..|.+..     .++|||||+|.+.++|++||.  +++.|.|+.|.|.+|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            3467999999999999999999999999999987654     358999999999999999985  889999999999999


Q ss_pred             cCCCC
Q 013837          372 TASSG  376 (435)
Q Consensus       372 ~~~~~  376 (435)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77653

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.7e-17  Score=118.80  Aligned_cols=72  Identities=18%  Similarity=0.355  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccCCC
Q 013837          297 VFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATASS  375 (435)
Q Consensus       297 l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~~~  375 (435)
                      |||+|||.++|+++|+++|++|| +..+.+      +.++|||||+|.+.++|.+|++.|||..+.|+.|+|+|+....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444443      3458999999999999999999999999999999999996543

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=1.2e-17  Score=126.16  Aligned_cols=77  Identities=21%  Similarity=0.220  Sum_probs=70.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.+++++|+++|+.||.|+.+.|..       +|||||+|.+.++|.+||+.|||..|.|+.|+|.|+
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3456899999999999999999999999999998864       479999999999999999999999999999999998


Q ss_pred             cCCC
Q 013837          372 TASS  375 (435)
Q Consensus       372 ~~~~  375 (435)
                      ....
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            7543

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.2e-18  Score=128.69  Aligned_cols=87  Identities=49%  Similarity=0.887  Sum_probs=77.3

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v  253 (435)
                      +++|||+|||+.+|+++|+++|+.||.+..+.+. ....+.+..++.++|||||+|.+.++|..|++|||..|.|+.|+|
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~-~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQA-PGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   79 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCS-SSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCC
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEe-ccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEE
Confidence            4789999999999999999999999998776543 345577778889999999999999999999999999999999999


Q ss_pred             cCCCCCCc
Q 013837          254 RRPTDYNP  261 (435)
Q Consensus       254 ~~~~~~~~  261 (435)
                      .+++++.+
T Consensus        80 ~r~k~~~p   87 (90)
T d1u2fa_          80 RRPHDYQP   87 (90)
T ss_dssp             BCTTCCSC
T ss_pred             CCCCCCCC
Confidence            98887653

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.8e-17  Score=121.59  Aligned_cols=78  Identities=24%  Similarity=0.418  Sum_probs=70.6

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||..+++++|+++|.+||.            |..+.+..++|||||+|.+.++|..|+ .|+|..|.|
T Consensus        14 ~~~~~~~l~v~nL~~~~te~~L~~~F~~fG~------------i~~v~i~~~kg~afV~f~~~~~A~~Ai~~l~~~~i~g   81 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQ------------IMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEG   81 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHHhCC------------ceEEEEEecceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3345679999999999999999999999997            677788889999999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|+|.|+...
T Consensus        82 ~~l~v~~ak~~   92 (96)
T d1x4ga1          82 HVVKCYWGKES   92 (96)
T ss_dssp             EECEEECCCCC
T ss_pred             EEEEEEEcCCC
Confidence            99999998653

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=8.5e-18  Score=130.68  Aligned_cols=80  Identities=19%  Similarity=0.322  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      ....+|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++|.+||+ |||..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            456799999999999999999999999998776666666789999999999999999999997 9999999999999988


Q ss_pred             c
Q 013837          372 T  372 (435)
Q Consensus       372 ~  372 (435)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.68  E-value=1.8e-17  Score=121.08  Aligned_cols=78  Identities=15%  Similarity=0.378  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      |+|||+|||+.+|+++|+++|+.||.|..+.      .+.+...+.++|||||+|.+.++|.+|+ .|||..|.|++|.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~------~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V   75 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSI------RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT   75 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEE------ECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeee------eecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            7999999999999999999999999864321      1233456778999999999999999999 59999999999999


Q ss_pred             cCCCC
Q 013837          254 RRPTD  258 (435)
Q Consensus       254 ~~~~~  258 (435)
                      .++.+
T Consensus        76 ~~a~P   80 (81)
T d2ghpa1          76 KVSNP   80 (81)
T ss_dssp             EECCC
T ss_pred             EEccC
Confidence            98754

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.68  E-value=8.8e-18  Score=123.10  Aligned_cols=79  Identities=15%  Similarity=0.241  Sum_probs=65.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      .++|||+|||+.+|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..|.|++|.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~------i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~   75 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCR------IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK   75 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEE------CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceee------eeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            46899999999999999999999999854421      1222234456899999999999999999 6999999999999


Q ss_pred             EcCCCC
Q 013837          253 VRRPTD  258 (435)
Q Consensus       253 v~~~~~  258 (435)
                      |.|+.+
T Consensus        76 v~~a~p   81 (82)
T d1b7fa1          76 VSYARP   81 (82)
T ss_dssp             EEECCC
T ss_pred             EEEcCC
Confidence            998753

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=2.3e-18  Score=124.01  Aligned_cols=76  Identities=12%  Similarity=0.248  Sum_probs=65.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEc
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVR  254 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~  254 (435)
                      |+|||+|||+++|+++|+++|++||.|..+.      ++.+..++.++|||||+|.+.++|.+|++++++.|+|+.|.|+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~   74 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECL------VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   74 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEE------EECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceee------eecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEE
Confidence            6899999999999999999999999875421      2333445778999999999999999999999999999999998


Q ss_pred             CC
Q 013837          255 RP  256 (435)
Q Consensus       255 ~~  256 (435)
                      .|
T Consensus        75 ~A   76 (77)
T d1uawa_          75 VA   76 (77)
T ss_dssp             EC
T ss_pred             EC
Confidence            64

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=6.8e-17  Score=119.69  Aligned_cols=78  Identities=14%  Similarity=0.092  Sum_probs=69.7

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh--CCceeCCeEEE
Q 013837          291 AEGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL--NGLKMGDKTLT  367 (435)
Q Consensus       291 ~~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l--~g~~~~g~~l~  367 (435)
                      ..+.++|||+|||.. +|++||.++|++||.|..|.|+.+      +++|||+|++.++|..|++.|  ++..+.|++|+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            356789999999986 889999999999999999999876      468999999999999999966  68899999999


Q ss_pred             EEEccCC
Q 013837          368 VRRATAS  374 (435)
Q Consensus       368 V~~a~~~  374 (435)
                      |.||+..
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999643

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.67  E-value=3.2e-17  Score=124.14  Aligned_cols=78  Identities=14%  Similarity=0.229  Sum_probs=69.9

Q ss_pred             CCCCeEEEcCCCCC-CCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHH--HhCCceeCCeEEEE
Q 013837          292 EGPDRVFVGGLPYY-FTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACA--ALNGLKMGDKTLTV  368 (435)
Q Consensus       292 ~~~~~l~V~nLp~~-~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~--~l~g~~~~g~~l~V  368 (435)
                      ...++|||+|||.. +|+++|.++|+.||.|..|.|+++      +|||||+|.+.++|..|++  .+++..|.|+.|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            45678999999985 899999999999999999999865      5799999999999999997  47899999999999


Q ss_pred             EEccCCC
Q 013837          369 RRATASS  375 (435)
Q Consensus       369 ~~a~~~~  375 (435)
                      .||+.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9996553

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=9.6e-18  Score=127.82  Aligned_cols=83  Identities=19%  Similarity=0.337  Sum_probs=68.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+++|+++|+++|.+||.|..+.      ++.+..++.++|||||+|.+.++|.+||+++++.|.|+.|
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~------i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i   91 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCV------VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVV   91 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEE------EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCccccee------ecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEE
Confidence            3457999999999999999999999999864411      0111224568899999999999999999999999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++.+..
T Consensus        92 ~V~~a~~ke  100 (103)
T d1x4ba1          92 EPKRAVARE  100 (103)
T ss_dssp             EEECCSSCC
T ss_pred             EEEECcccC
Confidence            999877543

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.3e-17  Score=124.09  Aligned_cols=81  Identities=22%  Similarity=0.340  Sum_probs=69.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+++|+++|+++|+.||.|..+.+      +.+..++.++|||||+|.+.++|..|+ .||+..|+|++|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i------~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l   77 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI------PLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   77 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEEC------CCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEeccc------ccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            4579999999999999999999999998765322      233345778999999999999999999 699999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++.+.
T Consensus        78 ~v~~a~p~   85 (89)
T d2cqba1          78 RVNLAKPM   85 (89)
T ss_dssp             EEEECCCC
T ss_pred             EEEEeCCC
Confidence            99998643

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.67  E-value=8.9e-17  Score=130.27  Aligned_cols=83  Identities=16%  Similarity=0.245  Sum_probs=67.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+++|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|..|| .|||..|+|+.
T Consensus        40 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~  113 (139)
T d1u6fa1          40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK------IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR  113 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEE------EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccc------cccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEE
Confidence            3457899999999999999999999999864311      1112223567899999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus       114 l~V~~a~~~~  123 (139)
T d1u6fa1         114 LKVALAASGH  123 (139)
T ss_dssp             EEEEESSCCC
T ss_pred             EEEEEcCCCC
Confidence            9999986543

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=4.2e-18  Score=129.47  Aligned_cols=79  Identities=24%  Similarity=0.329  Sum_probs=66.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|.+|++|||..|.|+.|
T Consensus        16 ~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~------i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l   89 (101)
T d2cq4a1          16 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR------IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPI   89 (101)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEE------ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEE------eeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEE
Confidence            4568999999999999999999999999864421      1222334678999999999999999999999999999999


Q ss_pred             EEcCC
Q 013837          252 RVRRP  256 (435)
Q Consensus       252 ~v~~~  256 (435)
                      .|.++
T Consensus        90 ~V~~a   94 (101)
T d2cq4a1          90 IVQAS   94 (101)
T ss_dssp             EEEEH
T ss_pred             EEEEC
Confidence            99865

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1e-17  Score=122.88  Aligned_cols=79  Identities=24%  Similarity=0.368  Sum_probs=66.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..++|||+|||+++|+++|.++|+.||.|..+.      .+.+..++.++|||||+|.+.++|.+|++++++.|.|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~   78 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV------VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVE   78 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhcccccee------ecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEE
Confidence            457899999999999999999999999864421      12222346678999999999999999999999999999999


Q ss_pred             EcCCC
Q 013837          253 VRRPT  257 (435)
Q Consensus       253 v~~~~  257 (435)
                      |.+|.
T Consensus        79 V~~A~   83 (84)
T d1l3ka1          79 PKRAV   83 (84)
T ss_dssp             EEECC
T ss_pred             EEeee
Confidence            98763

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.3e-17  Score=124.99  Aligned_cols=82  Identities=26%  Similarity=0.388  Sum_probs=68.4

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||..+|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|.+|+ .|||..|.|++|
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~------~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   81 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM------PKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI   81 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccce------eecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            3579999999999999999999999998544211      222234667899999999999999999 699999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      +|.++.+..
T Consensus        82 ~V~~A~~~~   90 (93)
T d1x5ua1          82 RVNKASAHN   90 (93)
T ss_dssp             EEEETTTTS
T ss_pred             EEEEcCCCC
Confidence            999987543

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.1e-17  Score=119.88  Aligned_cols=75  Identities=16%  Similarity=0.352  Sum_probs=63.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      +|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|.+||++++..|.|+.|.|.+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i------~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~r   74 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTL------KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKR   74 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhcccccccc------ccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeE
Confidence            5999999999999999999999998644221      2222345678999999999999999999999999999999976


Q ss_pred             C
Q 013837          256 P  256 (435)
Q Consensus       256 ~  256 (435)
                      +
T Consensus        75 A   75 (75)
T d1hd0a_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.1e-16  Score=118.25  Aligned_cols=75  Identities=24%  Similarity=0.399  Sum_probs=66.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||+.+|+++|+++|+.||.+            ..+.+..++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i------------~~~~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i   74 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPG------------AVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPI   74 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTT------------CEEEEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhccccee------------eeEEEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            45789999999999999999999999874            33455668999999999999999999 699999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.|+.+.
T Consensus        75 ~V~~akP~   82 (86)
T d2cpda1          75 EVTLAKPV   82 (86)
T ss_dssp             EEECCCCC
T ss_pred             EEEeccCC
Confidence            99998654

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.8e-17  Score=126.50  Aligned_cols=82  Identities=17%  Similarity=0.279  Sum_probs=68.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      +.++|||+|||+.+|+++|+++|..||.|+.+.      .+.+..++.++|||||+|.+.++|..|| .|||..|.|++|
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~------~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i   90 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK------VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   90 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEE------EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccc------eeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEE
Confidence            356899999999999999999999999865421      1222234567899999999999999999 699999999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++....
T Consensus        91 ~V~~a~~k~   99 (102)
T d2cpza1          91 KVQLKRSKN   99 (102)
T ss_dssp             EEECCCCSC
T ss_pred             EEEEeCCCC
Confidence            999987653

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.8e-16  Score=121.27  Aligned_cols=81  Identities=16%  Similarity=0.270  Sum_probs=72.6

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ++++|||+|||..+|+++|.++|..||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..|.|++|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~------~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l   90 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP------IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSC------CEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEE------eecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            468999999999999999999999999987643      3556677889999999999999999999 699999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.|+...
T Consensus        91 ~V~~ak~k   98 (102)
T d2cpxa1          91 VIEFGKNK   98 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEeCCCc
Confidence            99998754

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.4e-17  Score=124.87  Aligned_cols=81  Identities=22%  Similarity=0.286  Sum_probs=66.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..+++|||+|||+++|+++|+++|..||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..|.|++
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   78 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKII------MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI   78 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceec------cccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4678999999999999999999999999854311      0111123456789999999999999999 59999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.|+..
T Consensus        79 i~V~~a~~   86 (93)
T d1h2vz_          79 IRTDWDAG   86 (93)
T ss_dssp             CEEEEESC
T ss_pred             EEEEEcCC
Confidence            99998654

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=2.8e-16  Score=116.88  Aligned_cols=77  Identities=27%  Similarity=0.402  Sum_probs=66.2

Q ss_pred             cccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHH-HhCCce
Q 013837          171 TRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGII  245 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~-~l~~~~  245 (435)
                      ....++|||+|||..+|+++|+++|+.||.|.            .+.+    ...+|||||+|.+.++|..|+ .++|..
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~------------~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~   72 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK------------SCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRK   72 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEE------------EEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCce------------eeeeecccCccceeeEEEECCHHHHHHHHHHcCCCE
Confidence            34578999999999999999999999999853            3332    335799999999999999999 599999


Q ss_pred             ecCceEEEcCCCCC
Q 013837          246 FEGVAVRVRRPTDY  259 (435)
Q Consensus       246 ~~g~~l~v~~~~~~  259 (435)
                      |.|+.|+|.|+...
T Consensus        73 ~~g~~i~v~~a~~~   86 (90)
T d2cqia1          73 ILGKEVKVNWATTP   86 (90)
T ss_dssp             ETTEEEEEEECCCT
T ss_pred             ECCEEEEEEEcCCC
Confidence            99999999998643

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.9e-17  Score=123.61  Aligned_cols=82  Identities=26%  Similarity=0.421  Sum_probs=67.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.++|||+|||+.+|+++|.++|..||.|..+.      .+.....+.++|||||+|.+.++|..|+ .|+|..|+|++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~------~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~   76 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVV------VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQ   76 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEE------ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhcccccccee------eccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3567899999999999999999999999864421      1122234567899999999999999999 69999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++...
T Consensus        77 l~V~~a~~~   85 (90)
T d1x5sa1          77 IRVDQAGKS   85 (90)
T ss_dssp             CEEEEEECC
T ss_pred             EEEEEcCCC
Confidence            999987543

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=9.2e-17  Score=120.90  Aligned_cols=79  Identities=28%  Similarity=0.412  Sum_probs=67.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..         +........++||||+|.+.++|..|| .||++.|.|++
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~---------~~~~~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~   82 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRD---------IDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR   82 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEE---------EEECCSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEE---------EEecccccccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            45678999999999999999999999997532         222233457899999999999999999 59999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |+|.++...
T Consensus        83 l~V~~a~~~   91 (95)
T d1x4aa1          83 LRVEFPRSG   91 (95)
T ss_dssp             CEEECCCCC
T ss_pred             EEEEeccCC
Confidence            999998653

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.65  E-value=1.2e-17  Score=123.92  Aligned_cols=81  Identities=21%  Similarity=0.177  Sum_probs=66.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      .+.++|||+|||..+|+++|.++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|+.
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~------i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~   78 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   78 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccccc------ccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEE
Confidence            3567999999999999999999999999864411      1111223567899999999999999999 59999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.|+..
T Consensus        79 l~V~~a~~   86 (88)
T d1rk8a_          79 IQVDWCFV   86 (88)
T ss_dssp             CEEEESEE
T ss_pred             EEEEEecC
Confidence            99998753

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=3.1e-17  Score=124.57  Aligned_cols=83  Identities=24%  Similarity=0.310  Sum_probs=68.3

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ..+++|||+|||+.+|+++|+++|..||.|..+.+      +.+..++.++|||||+|.+.++|..|| .||+..|.|++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i------~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~   79 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHY------PIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRM   79 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEEC------CCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeee------cccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            35678999999999999999999999998543211      122234567899999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        80 i~V~~a~~~~   89 (99)
T d1whwa_          80 LHVLPSTIKK   89 (99)
T ss_dssp             EEEEECCCCS
T ss_pred             EEEEECCCCC
Confidence            9999887543

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=9.4e-17  Score=125.43  Aligned_cols=76  Identities=17%  Similarity=0.138  Sum_probs=66.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      .+++|||+|||..+|+++|.++|+.||.|..         |.....+.++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~---------i~~~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   76 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---------IRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYL   76 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEE---------EEEECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCeEe---------ecccccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            4679999999999999999999999998644         333445667999999999999999999 699999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      .|.++.
T Consensus        77 ~V~~a~   82 (114)
T d2f9da1          77 VVLYYN   82 (114)
T ss_dssp             EEEECC
T ss_pred             EEEEcC
Confidence            999864

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1.6e-17  Score=120.85  Aligned_cols=76  Identities=20%  Similarity=0.323  Sum_probs=63.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      +|||+|||+.+|+++|+++|..||.|..+.      ++.+..++.++|||||+|.+.++|..|+ .|+|..+.|++|+|.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~   75 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIR------VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   75 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEE
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEE------EEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            699999999999999999999999864311      1111223556799999999999999999 699999999999999


Q ss_pred             CCC
Q 013837          255 RPT  257 (435)
Q Consensus       255 ~~~  257 (435)
                      |+.
T Consensus        76 ~a~   78 (80)
T d1cvja1          76 WSQ   78 (80)
T ss_dssp             ECC
T ss_pred             EeC
Confidence            874

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=2.6e-17  Score=121.46  Aligned_cols=81  Identities=12%  Similarity=0.120  Sum_probs=64.5

Q ss_pred             cCCeEEEcCCCCCCC-HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          173 HARRVYVGGLPPLAN-EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t-~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      +.++|||+|||+++| +++|+++|++||.|..+.+.     ..+...+.++|||||+|.+.++|.+|++||+..|.|+.|
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~-----~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l   77 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIP-----AGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREI   77 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECC-----SCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeee-----cccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEE
Confidence            468999999999976 56799999999986542210     111234567899999999999999999999999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        78 ~V~~a~~   84 (86)
T d2ghpa3          78 SVSLADK   84 (86)
T ss_dssp             EEEECCC
T ss_pred             EEEEcCC
Confidence            9998764

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.3e-17  Score=120.84  Aligned_cols=78  Identities=15%  Similarity=0.275  Sum_probs=64.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      .+|||+|||..+|+++|+++|++||.|..+.      .+.+...+..+|||||+|.+.++|..|+ .|||..|.|++|.|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~------i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v   76 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCK------LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV   76 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCccccc------ceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4699999999999999999999999854311      0111123456799999999999999999 69999999999999


Q ss_pred             cCCCC
Q 013837          254 RRPTD  258 (435)
Q Consensus       254 ~~~~~  258 (435)
                      .++.+
T Consensus        77 ~~AkP   81 (82)
T d1fxla1          77 SYARP   81 (82)
T ss_dssp             EECCC
T ss_pred             EEeeC
Confidence            98753

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=3.5e-17  Score=120.09  Aligned_cols=78  Identities=17%  Similarity=0.321  Sum_probs=65.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcC
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~  255 (435)
                      |||+|||+++|+++|+++|.+||.|....     .++.+..++.++|||||+|.+.++|..|+ .|+|..|.|++|.|.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~-----~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~   75 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTP-----KIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   75 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCC-----EECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeE-----EEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEE
Confidence            79999999999999999999999875421     01222234677899999999999999999 5999999999999998


Q ss_pred             CCCC
Q 013837          256 PTDY  259 (435)
Q Consensus       256 ~~~~  259 (435)
                      +.+.
T Consensus        76 a~~k   79 (83)
T d1x5ta1          76 AFKK   79 (83)
T ss_dssp             SCCC
T ss_pred             ecCC
Confidence            7654

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.3e-17  Score=124.28  Aligned_cols=82  Identities=16%  Similarity=0.229  Sum_probs=67.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|.+|+ .|+|..|.|+.
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~------i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~   79 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIY------LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   79 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccccc------ccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEE
Confidence            4567999999999999999999999999864421      1111124567899999999999999999 59999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.|+.+.
T Consensus        80 i~v~~akp~   88 (90)
T d2cq0a1          80 LNVEWAKPS   88 (90)
T ss_dssp             CEEEESSCC
T ss_pred             EEEEeeeCC
Confidence            999998653

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=4.6e-17  Score=117.69  Aligned_cols=75  Identities=17%  Similarity=0.172  Sum_probs=62.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEc
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVR  254 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~  254 (435)
                      +|||+|||+.+|+++|+++|.+||.|..+.+       .....+.++|||||+|.+.++|..|+ .|||..|+|++|.|.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i-------~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~   74 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAV-------HYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ   74 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEE-------SCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEE-------EEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            5999999999999999999999998543211       11124557899999999999999999 599999999999998


Q ss_pred             CCC
Q 013837          255 RPT  257 (435)
Q Consensus       255 ~~~  257 (435)
                      ++.
T Consensus        75 ~a~   77 (78)
T d1no8a_          75 LVT   77 (78)
T ss_dssp             EEC
T ss_pred             Eee
Confidence            754

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.2e-17  Score=120.03  Aligned_cols=77  Identities=17%  Similarity=0.292  Sum_probs=63.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEE
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v  253 (435)
                      .++|||+|||+++|+++|+++|+.||.|..+.      .+.+...+.++|||||+|.+.++|.+|++++|..|+|++|.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~------~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V   75 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE------IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV   75 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccc------cccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEE
Confidence            37899999999999999999999999864311      011112345679999999999999999999999999999999


Q ss_pred             cCC
Q 013837          254 RRP  256 (435)
Q Consensus       254 ~~~  256 (435)
                      ++|
T Consensus        76 ~~A   78 (79)
T d1l3ka2          76 RKA   78 (79)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            864

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=3.3e-17  Score=117.83  Aligned_cols=75  Identities=15%  Similarity=0.280  Sum_probs=64.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      +|||+|||+++|+++|+++|+.||.+..+.+      +.+..++..+|||||+|.+.++|.+|+++||+.|.|++|.|++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~------~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~   74 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAML------MFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKK   74 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECC------BCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEE
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeee------eeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEE
Confidence            5999999999999999999999998755321      2233346678999999999999999999999999999999986


Q ss_pred             C
Q 013837          256 P  256 (435)
Q Consensus       256 ~  256 (435)
                      |
T Consensus        75 A   75 (75)
T d2msta_          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=9.3e-17  Score=122.40  Aligned_cols=78  Identities=12%  Similarity=0.084  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCCCCCC-C----HHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEE
Q 013837          292 EGPDRVFVGGLPYYF-T----ETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTL  366 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~-t----e~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l  366 (435)
                      ....+|||+||+..+ +    +++|.++|+.||.|..+.+++.      +|||||+|.+.++|.+|++.|||..|+|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            345789999999876 3    3579999999999999998753      6799999999999999999999999999999


Q ss_pred             EEEEccCCC
Q 013837          367 TVRRATASS  375 (435)
Q Consensus       367 ~V~~a~~~~  375 (435)
                      +|.||....
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999997654

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.9e-17  Score=120.66  Aligned_cols=81  Identities=21%  Similarity=0.313  Sum_probs=66.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....+|||+|||+++|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|.+||+ +...|+|+.|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i   78 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQ------VKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWC   78 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEE------EEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEE
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceee------eccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEe
Confidence            4567899999999999999999999999865421      12222356788999999999999999996 4568999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++.+.
T Consensus        79 ~v~~a~~k   86 (90)
T d2cqga1          79 DCKLPNSK   86 (90)
T ss_dssp             EEECCCTT
T ss_pred             EEEeCCCC
Confidence            99988654

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=3.3e-17  Score=120.18  Aligned_cols=75  Identities=24%  Similarity=0.313  Sum_probs=62.3

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      +.++|||+|||+.+|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|..|+ .||+..|.|++|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~------i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i   81 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVS------IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   81 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEE------EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCcccc------ccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEe
Confidence            467899999999999999999999999864311      1111223566899999999999999999 699999999999


Q ss_pred             EE
Q 013837          252 RV  253 (435)
Q Consensus       252 ~v  253 (435)
                      +|
T Consensus        82 ~V   83 (83)
T d2cqca1          82 RV   83 (83)
T ss_dssp             EE
T ss_pred             EC
Confidence            87

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=1e-16  Score=124.66  Aligned_cols=77  Identities=21%  Similarity=0.156  Sum_probs=69.9

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||+.+++++|+++|..||.            |..+.+..++|||||+|.+.++|.+|| .|||..|.|
T Consensus         6 ~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~------------I~~v~l~~~kg~afV~f~~~~~A~~A~~~lng~~~~g   73 (111)
T d1whxa_           6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGS------------LGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFHH   73 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSC------------EEEEECCSSSSCEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhhccCC------------ccEEEeeccCceEEEEEcCHHHHHHHHHHHcCCccCC
Confidence            3455679999999999999999999999997            677888889999999999999999999 699999999


Q ss_pred             ceEEEcCCCC
Q 013837          249 VAVRVRRPTD  258 (435)
Q Consensus       249 ~~l~v~~~~~  258 (435)
                      +.|.|.|+..
T Consensus        74 r~l~v~~a~~   83 (111)
T d1whxa_          74 VPLYLEWAPI   83 (111)
T ss_dssp             SBCEEEEEET
T ss_pred             CeEEEEECCC
Confidence            9999998654

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.8e-17  Score=117.45  Aligned_cols=75  Identities=17%  Similarity=0.276  Sum_probs=62.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcC
Q 013837          176 RVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRR  255 (435)
Q Consensus       176 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~  255 (435)
                      +|||+|||+++|+++|+++|++||.|..+.+      +.+..++.++|||||+|.+.++|.+||+.+++.|+|+.|.|+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i------~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~   74 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIEL------PMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKV   74 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEEC------CCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEEC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccc------cccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEE
Confidence            5999999999999999999999998644221      1222345678999999999999999998888999999999975


Q ss_pred             C
Q 013837          256 P  256 (435)
Q Consensus       256 ~  256 (435)
                      |
T Consensus        75 A   75 (75)
T d1x0fa1          75 A   75 (75)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=7.8e-17  Score=117.00  Aligned_cols=73  Identities=19%  Similarity=0.346  Sum_probs=62.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCc-eecCceEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGI-IFEGVAVR  252 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~-~~~g~~l~  252 (435)
                      .+|||+|||.++|+++|+++|.+||.++.            ..+...+|||||+|.+.++|..|+ .|||. .+.|++|.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~------------~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~   69 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLA------------GQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   69 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCS------------SCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEE------------eEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEE
Confidence            47999999999999999999999997543            222335899999999999999999 69985 69999999


Q ss_pred             EcCCCCC
Q 013837          253 VRRPTDY  259 (435)
Q Consensus       253 v~~~~~~  259 (435)
                      |.++.+.
T Consensus        70 V~~a~~k   76 (80)
T d2cqha1          70 VDYSVSK   76 (80)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCc
Confidence            9998754

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.6e-17  Score=121.02  Aligned_cols=79  Identities=18%  Similarity=0.237  Sum_probs=65.8

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ..++|||+|||..+|+++|.++|+.||.|..+.       +.....+.++|||||+|.+.++|.+||++++..|.|+.|.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~-------l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~   77 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ-------MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLL   77 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEE-------EEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccce-------eeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEE
Confidence            467999999999999999999999999864411       1111234567999999999999999999999999999999


Q ss_pred             EcCCCC
Q 013837          253 VRRPTD  258 (435)
Q Consensus       253 v~~~~~  258 (435)
                      |.+..+
T Consensus        78 v~~~~d   83 (85)
T d1zh5a2          78 ILFKDD   83 (85)
T ss_dssp             EEEGGG
T ss_pred             EEEcCC
Confidence            987654

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=8.9e-17  Score=118.38  Aligned_cols=75  Identities=29%  Similarity=0.503  Sum_probs=67.7

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ..++|||+|||.++++++|+++|+.||.            |..+.+..++|||||+|.+.++|..|+ .|||..|.|+.|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~------------i~~i~~~~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l   74 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGK------------AGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQL   74 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCC------------CSEEEEETTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCC------------ceEeeeecccceEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3468999999999999999999999997            556667788999999999999999999 599999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.|+...
T Consensus        75 ~V~~A~~~   82 (86)
T d2cpja1          75 RVRFACHS   82 (86)
T ss_dssp             EEEESSCC
T ss_pred             EEEECCCc
Confidence            99997653

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=1.5e-16  Score=115.22  Aligned_cols=74  Identities=23%  Similarity=0.377  Sum_probs=66.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+||+  +|+++|+++|++||.            |.++.+...+|||||+|.+.++|..|+ .|||..|.|++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~------------I~~v~~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~   68 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGN------------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQ   68 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCC------------CSCEEEETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCc------------cceeeeccCCCEEEEEEcccHHHHHHHHHhCCCEECCEE
Confidence            456799999995  899999999999997            455667788999999999999999999 69999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |+|.|+.+.
T Consensus        69 l~V~~a~~~   77 (79)
T d2bz2a1          69 LKVNIARKQ   77 (79)
T ss_dssp             CEEEECCSS
T ss_pred             EEEEEecCC
Confidence            999998643

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.5e-17  Score=121.21  Aligned_cols=79  Identities=22%  Similarity=0.370  Sum_probs=66.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-hCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-LDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l~~~~~~g~~l~v  253 (435)
                      .+|||+|||..+|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+. |||..|.|++|.|
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~------i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V   75 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFN------LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV   75 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEE------EECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEE------eeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4799999999999999999999999864421      12222346789999999999999999995 9999999999999


Q ss_pred             cCCCCC
Q 013837          254 RRPTDY  259 (435)
Q Consensus       254 ~~~~~~  259 (435)
                      .++...
T Consensus        76 ~~A~~~   81 (85)
T d2u2fa_          76 QRASVG   81 (85)
T ss_dssp             EECCCC
T ss_pred             EECCCC
Confidence            998643

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=3.2e-16  Score=112.01  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcC
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRR  255 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~  255 (435)
                      |||+|||+++++++|+++|.+||             +..+.++.++|||||+|.+.++|.+|+ .|||..+.|++|.|.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-------------~~~~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~   67 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-------------LKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQL   67 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-------------ccceeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEE
Confidence            79999999999999999999997             566778889999999999999999999 6999999999999998


Q ss_pred             CCC
Q 013837          256 PTD  258 (435)
Q Consensus       256 ~~~  258 (435)
                      +..
T Consensus        68 a~~   70 (75)
T d1wi6a1          68 QPT   70 (75)
T ss_dssp             CCS
T ss_pred             eCC
Confidence            753

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.63  E-value=8.6e-17  Score=121.32  Aligned_cols=79  Identities=16%  Similarity=0.254  Sum_probs=68.7

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||+.+|+++|+++|..||.|.           .....+.++|||||+|.+.++|..|+ .||+..|.|
T Consensus        12 ~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~-----------~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g   80 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----------LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEEC-----------CEEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcccce-----------eeeecCccccEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            345678999999999999999999999999752           22345678999999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|.|.|+.+.
T Consensus        81 r~i~V~~a~~k   91 (96)
T d1fjca_          81 RSVSLYYTGEK   91 (96)
T ss_dssp             EEEEEEECSSS
T ss_pred             EEEEEEEeCCC
Confidence            99999998754

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.63  E-value=2.2e-16  Score=120.52  Aligned_cols=89  Identities=21%  Similarity=0.215  Sum_probs=70.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCce--EEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAV--VNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v--~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      ....+|||+|||..+|+++|.++|..||.|..+.+.......  .+..++.++|||||+|.+.++|..|| .|||..|.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            456799999999999999999999999987654332221111  11123566899999999999999999 599999999


Q ss_pred             ceEEEcCCCCCC
Q 013837          249 VAVRVRRPTDYN  260 (435)
Q Consensus       249 ~~l~v~~~~~~~  260 (435)
                      ++|.|.++....
T Consensus        86 r~i~V~~a~~~~   97 (101)
T d2cpea1          86 SKLKVSLARKKP   97 (101)
T ss_dssp             EECEEECSSCCC
T ss_pred             EEEEEEEcCCCC
Confidence            999999987653

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.5e-17  Score=126.40  Aligned_cols=83  Identities=31%  Similarity=0.448  Sum_probs=68.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ...++|||+|||+++|+++|.++|+.||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|++..|.|+.
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~------i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~   79 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFR------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA   79 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEE------EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccc------cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            4567999999999999999999999999865421      1112223556899999999999999999 59999999999


Q ss_pred             EEEcCCCCCC
Q 013837          251 VRVRRPTDYN  260 (435)
Q Consensus       251 l~v~~~~~~~  260 (435)
                      |.|.++....
T Consensus        80 i~V~~a~~~~   89 (104)
T d1p1ta_          80 LRVDNAASEK   89 (104)
T ss_dssp             BEEEETTCTT
T ss_pred             EEEEECCCCC
Confidence            9999976543

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.62  E-value=4.7e-16  Score=116.58  Aligned_cols=82  Identities=20%  Similarity=0.241  Sum_probs=67.2

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEE-EEecCCCcEEEEEecCHHHHHHHH-Hh-CCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVN-VYINHEKKFAFVEMRTVEEASNAM-AL-DGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~-~~~~~~~g~afv~f~~~~~a~~a~-~l-~~~~~~g  248 (435)
                      ....+|||+|||+.+++++|+++|..||.|..+.+      +.+ ..++.++|||||+|.+.++|..|+ .| |+..|.|
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i------~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~G   79 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRL------PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   79 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEE------EeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECC
Confidence            35678999999999999999999999998644221      111 113567899999999999999999 56 8999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|.|.|+...
T Consensus        80 r~l~V~~A~~~   90 (94)
T d2cpha1          80 RRLVLEWADSE   90 (94)
T ss_dssp             CBCEEEECCCC
T ss_pred             EEEEEEEcCCC
Confidence            99999998754

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4e-16  Score=115.63  Aligned_cols=76  Identities=22%  Similarity=0.363  Sum_probs=65.5

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee-cCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF-EGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~-~g~~  250 (435)
                      ++++|||+|||..+|+++|+++|..||.|+          ......+.++|||||+|.+.++|..|+ .|+|..+ .|++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~----------~~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~   78 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVV----------KGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHH   78 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCE----------EEEEECSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEE----------EEEEeeecccceeEEEECCHHHHHHHHHhccCCEecCCCE
Confidence            467999999999999999999999999752          223345677899999999999999999 6999988 5899


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |+|.|++.
T Consensus        79 l~v~~sk~   86 (88)
T d2adca2          79 LRVSFSKS   86 (88)
T ss_dssp             CEEEECSS
T ss_pred             EEEEeCCC
Confidence            99998754

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.2e-16  Score=118.16  Aligned_cols=82  Identities=21%  Similarity=0.314  Sum_probs=67.2

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .....++|||+|||+.+|+++|+++|..||.|..+        .+......++|||||+|.+.++|.+|+ .||+..|.|
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v--------~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g   78 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDV--------EIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEG   78 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEE--------EEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeec--------cccccccCCcceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            34456789999999999999999999999975331        111112346899999999999999999 699999999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      +.|.|.++.+.
T Consensus        79 ~~l~V~~A~~r   89 (93)
T d2cq3a1          79 RKIEVNNATAR   89 (93)
T ss_dssp             EECEEEECCSS
T ss_pred             EEEEEEecCcC
Confidence            99999998754

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.3e-16  Score=118.03  Aligned_cols=74  Identities=23%  Similarity=0.316  Sum_probs=65.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      .+.+|||+|||+++++++|+++|.+||.             ..+.+...+|||||+|.+.++|.+|+ .||++.|.|+.|
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G~-------------~~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l   70 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYDL-------------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL   70 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-------------CCEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-------------eeeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            3568999999999999999999999972             23455678999999999999999999 699999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        71 ~V~~a~~~   78 (88)
T d1wg1a_          71 IVQLQPTD   78 (88)
T ss_dssp             EEEECCCC
T ss_pred             EEEEcCCC
Confidence            99987543

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=6.6e-17  Score=118.92  Aligned_cols=78  Identities=23%  Similarity=0.376  Sum_probs=63.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      ..++|||+|||+.+|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .|||..+.|  +
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~------i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~   78 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSR------ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATE   78 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccc------cccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCE
Confidence            457899999999999999999999999864311      1111123567899999999999999999 699999998  5


Q ss_pred             eEEEcCC
Q 013837          250 AVRVRRP  256 (435)
Q Consensus       250 ~l~v~~~  256 (435)
                      +|.|.|+
T Consensus        79 ~i~V~~A   85 (85)
T d1fxla2          79 PITVKFA   85 (85)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEeC
Confidence            6888874

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=9.6e-18  Score=125.13  Aligned_cols=78  Identities=22%  Similarity=0.439  Sum_probs=68.4

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEe-----ecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLV-----KDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVR  369 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~-----~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~  369 (435)
                      ++|||+|||..+|+++|+++|+.||.|..+.+.     .+..++.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            589999999999999999999999988766543     344578899999999999999999996 99999999999998


Q ss_pred             EccC
Q 013837          370 RATA  373 (435)
Q Consensus       370 ~a~~  373 (435)
                      .++.
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.61  E-value=6e-17  Score=123.50  Aligned_cols=75  Identities=13%  Similarity=0.163  Sum_probs=70.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEc
Q 013837          296 RVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRA  371 (435)
Q Consensus       296 ~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a  371 (435)
                      .++|.+++..++|++|.++|++||.|+.|.|+.+ .+|.++|||||+|.+.++|.+|+..|||.+|+|+.|.|+|+
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            5788899989999999999999999999999877 57999999999999999999999999999999999999986

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=6.4e-16  Score=114.66  Aligned_cols=75  Identities=21%  Similarity=0.351  Sum_probs=64.7

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe----cCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI----NHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~----~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      ...+|||+|||+.+|+++|+++|..||.|.            .+.+    +.++|||||+|.+.++|..|+ .|||..|+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~------------~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~   74 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNIL------------SCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLN   74 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEE------------EEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCce------------EEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEEC
Confidence            345799999999999999999999999753            3332    335799999999999999999 69999999


Q ss_pred             CceEEEcCCCCC
Q 013837          248 GVAVRVRRPTDY  259 (435)
Q Consensus       248 g~~l~v~~~~~~  259 (435)
                      |+.|.|.++...
T Consensus        75 g~~i~V~~a~~~   86 (89)
T d1cvja2          75 DRKVFVGRFKSR   86 (89)
T ss_dssp             TEEEEEEECCCT
T ss_pred             CEEEEEEECCCC
Confidence            999999988654

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.6e-16  Score=121.92  Aligned_cols=81  Identities=17%  Similarity=0.239  Sum_probs=64.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      +.++|||+|||+.+|+++|+++|+.|| ++.+.++     +.....+.++|||||+|.+.++|.+|+++|+..|.|+.|.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~-----~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~   87 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLP-----REPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIR   87 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECC-----BCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceee-----eeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEE
Confidence            458999999999999999999999998 3221100     1111234568999999999999998889999999999999


Q ss_pred             EcCCCCC
Q 013837          253 VRRPTDY  259 (435)
Q Consensus       253 v~~~~~~  259 (435)
                      |.++...
T Consensus        88 V~~a~~~   94 (104)
T d1wi8a_          88 VDVADQA   94 (104)
T ss_dssp             EEECCCC
T ss_pred             EEECCCC
Confidence            9987654

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=3.1e-16  Score=118.97  Aligned_cols=82  Identities=21%  Similarity=0.278  Sum_probs=65.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhC------Cc
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALD------GI  244 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~------~~  244 (435)
                      ...++|||+|||+.+|+++|+++|..||.|..+.+      +.+...+.++|||||+|.+.++|..|| .++      |.
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~------~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~   79 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRV------VLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEC------CBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeee------ccccccccccceEEEEEcCHHHHHHHHHHcccccccCCc
Confidence            45689999999999999999999999997533211      111223456899999999999999999 465      67


Q ss_pred             eecCceEEEcCCCCC
Q 013837          245 IFEGVAVRVRRPTDY  259 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~  259 (435)
                      .|.|+.|.|.++.+.
T Consensus        80 ~~~gr~l~v~~a~~k   94 (98)
T d1x4ha1          80 KLDGRQLKVDLAVTR   94 (98)
T ss_dssp             ESSSCEEEEECCCCC
T ss_pred             EECCEEEEEEECCCC
Confidence            899999999998754

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.59  E-value=4.5e-16  Score=111.26  Aligned_cols=73  Identities=19%  Similarity=0.220  Sum_probs=61.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEE-EecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNV-YINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~-~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v  253 (435)
                      .+|||+|||+.+++++|+++|..||.|..         +... ..+..++||||+|.+.++|.+|+.+++..|+|++|.|
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~---------v~~~~~~~~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V   71 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIH---------VDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIV   71 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEE---------EEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEE---------EEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEE
Confidence            37999999999999999999999998533         1111 1233568999999999999999999999999999999


Q ss_pred             cCC
Q 013837          254 RRP  256 (435)
Q Consensus       254 ~~~  256 (435)
                      ..+
T Consensus        72 ~~~   74 (75)
T d2ghpa2          72 SHL   74 (75)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            754

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=8.7e-16  Score=113.00  Aligned_cols=76  Identities=22%  Similarity=0.305  Sum_probs=62.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec---CCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~---~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      |||+|||+++|+++|+++|+.||.|..+.      ++.+...+   .++|||||+|.+.++|..|+ .|||..|+|+.|.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~------i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~   74 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCT------ISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   74 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEE------EEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccc------eecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            79999999999999999999999865421      11111111   24789999999999999999 6999999999999


Q ss_pred             EcCCCC
Q 013837          253 VRRPTD  258 (435)
Q Consensus       253 v~~~~~  258 (435)
                      |.++..
T Consensus        75 V~~a~~   80 (85)
T d2cpfa1          75 VRISER   80 (85)
T ss_dssp             EECSSC
T ss_pred             EEECCC
Confidence            998753

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.7e-15  Score=115.47  Aligned_cols=82  Identities=17%  Similarity=0.257  Sum_probs=64.8

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ...++|||+|||+.+|+++|+++|+.||.|..+.      ++.+..++.++|||||+|.+.++|.+|++..+..|.|++|
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~------i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l   81 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAV------VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKA   81 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEE------ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEEC
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhccccccee------ccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEE
Confidence            3456899999999999999999999999854321      1112234668999999999999999999633457999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        82 ~V~~a~~~   89 (103)
T d2cqda1          82 NVNLAYLG   89 (103)
T ss_dssp             EEEESTTT
T ss_pred             EEEEcCCC
Confidence            99987643

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.59  E-value=1.3e-15  Score=111.38  Aligned_cols=74  Identities=23%  Similarity=0.337  Sum_probs=64.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHH-HhCCceec-C
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFE-G  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~-~l~~~~~~-g  248 (435)
                      .++++|||+|||..+|+++|.++|..||.            |..+.+. ..+|||||+|.+.++|..|+ .|+|..|. |
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~v~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~   73 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPG------------FKEVRLVPNRHDIAFVEFTTELQSNAAKEALQGFKITPT   73 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTT------------EEEEEECTTTCSCEEEEESSHHHHHHHHHHHTTCBSSTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCcc------------EEEeeeecccceeEEEecCCHHHHHHHHHHhCCcEeCCC
Confidence            35689999999999999999999999997            5555543 45799999999999999999 59999884 6


Q ss_pred             ceEEEcCCC
Q 013837          249 VAVRVRRPT  257 (435)
Q Consensus       249 ~~l~v~~~~  257 (435)
                      ++|+|.|++
T Consensus        74 ~~i~v~~ak   82 (83)
T d2b0ga1          74 HAMKITFAK   82 (83)
T ss_dssp             CBCEEEECC
T ss_pred             cEEEEEEec
Confidence            899999875

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=3.8e-16  Score=115.60  Aligned_cols=75  Identities=23%  Similarity=0.378  Sum_probs=64.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEE-ecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVY-INHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~-~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      .+++|||+|||+.+|+++|+++|.+||.|            .++. ...+++||||+|.+.++|.+|+. +++.|.|++|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v------------~~v~~~~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l   70 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDV------------MDVFIPKPFRAFAFVTFADDQIAQSLCG-EDLIIKGISV   70 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCC------------CEEECCSSCCSCCEEECSCHHHHHHTTT-CEEEETTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCc------------eEEEEeeccCceEEEEECCHHHHHHHHh-CCCEECCEEe
Confidence            46799999999999999999999999974            3333 34578999999999999999995 8899999999


Q ss_pred             EEcCCCCCC
Q 013837          252 RVRRPTDYN  260 (435)
Q Consensus       252 ~v~~~~~~~  260 (435)
                      .|.++.+..
T Consensus        71 ~v~~a~~k~   79 (88)
T d1wf0a_          71 HISNAEPKH   79 (88)
T ss_dssp             EEECCCCCC
T ss_pred             EEEeCCCCC
Confidence            999986543

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=9.8e-17  Score=122.14  Aligned_cols=81  Identities=12%  Similarity=0.252  Sum_probs=66.2

Q ss_pred             hcccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC
Q 013837          170 ATRHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG  248 (435)
Q Consensus       170 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g  248 (435)
                      .+...++|||+|||+++|+++|+++|+.||.|..+.       +.....+.++|||||+|.+.++|.+|+ .|||..|.|
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~-------~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~g   86 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTR-------ILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT   86 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEE-------EEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhccccccee-------eecccccccccceeEEeCCHHHHHHHHHHhCCCEECC
Confidence            445678999999999999999999999999864310       111124456899999999999999999 699999999


Q ss_pred             ceEEEcCCC
Q 013837          249 VAVRVRRPT  257 (435)
Q Consensus       249 ~~l~v~~~~  257 (435)
                      +++.|.++.
T Consensus        87 r~~~v~~~~   95 (101)
T d1x5oa1          87 PPGVSAPTE   95 (101)
T ss_dssp             CTTSCCCSS
T ss_pred             cCCccCCCC
Confidence            999887654

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=2.9e-16  Score=117.12  Aligned_cols=76  Identities=18%  Similarity=0.381  Sum_probs=64.1

Q ss_pred             cCCeEEEcCCCCCCCHHHHHH----HHHHHHHhhcCCCCCCCCceEEEEe---cCCCcEEEEEecCHHHHHHHH-HhCCc
Q 013837          173 HARRVYVGGLPPLANEQAIAT----FFSQVMTAIGGNSAGPGDAVVNVYI---NHEKKFAFVEMRTVEEASNAM-ALDGI  244 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~----~f~~~G~i~~~~~~~~~~~v~~~~~---~~~~g~afv~f~~~~~a~~a~-~l~~~  244 (435)
                      +.++|||+|||+.+|+++|++    +|.+||.            |..+.+   +.++|||||+|.+.++|..|+ .+||.
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~------------i~~i~~~~~~~~~g~afV~F~~~~~A~~A~~~~~~~   69 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQ------------ILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGF   69 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSC------------EEEEECCHHHHHTTCEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccccc------------ccceEEeeeccCCCceEEEECCHHHHHHHHHHhCCC
Confidence            468999999999999999875    4677776            444444   446899999999999999999 69999


Q ss_pred             eecCceEEEcCCCCCC
Q 013837          245 IFEGVAVRVRRPTDYN  260 (435)
Q Consensus       245 ~~~g~~l~v~~~~~~~  260 (435)
                      .|.|+.|.|.|+....
T Consensus        70 ~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          70 PFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             EETTEECEEEECSSCC
T ss_pred             EECCEEEEEEEeCCCc
Confidence            9999999999987543

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.58  E-value=1.3e-16  Score=117.48  Aligned_cols=78  Identities=27%  Similarity=0.421  Sum_probs=63.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      ...+|||+|||..+|+++|+++|++||.|..+.      .+.+...+.++|||||+|.+.++|..|+ .||+..+.|  +
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~------~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   78 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN------ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ   78 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEE------EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeee------eecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCe
Confidence            346799999999999999999999999864311      1111223556799999999999999999 599999977  8


Q ss_pred             eEEEcCC
Q 013837          250 AVRVRRP  256 (435)
Q Consensus       250 ~l~v~~~  256 (435)
                      +|.|.||
T Consensus        79 ~l~V~~A   85 (85)
T d1b7fa2          79 PLSVRLA   85 (85)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEEC
Confidence            8999875

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=1.4e-15  Score=112.50  Aligned_cols=76  Identities=17%  Similarity=0.164  Sum_probs=68.6

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hCCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~~~~~~g  248 (435)
                      .++++|||+|||..+|+++|.++|++||.            |..+.+..+++||||+|.+.++|..|++   +++..+.|
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~------------i~~v~~~~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g   73 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGK------------VTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPHLRN   73 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcccc------------cccccccccceEEEEEeCCHHHHHHHHHHHccCCCccCC
Confidence            46789999999999999999999999986            6777888899999999999999999983   57889999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|.|.|++..
T Consensus        74 ~~l~v~~sk~~   84 (88)
T d2cq1a1          74 QPIYIQYSNHK   84 (88)
T ss_dssp             EECEEEECSCS
T ss_pred             CEEEEEECCCC
Confidence            99999998644

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.58  E-value=2.6e-15  Score=113.23  Aligned_cols=75  Identities=23%  Similarity=0.381  Sum_probs=67.7

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecC--c
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEG--V  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g--~  249 (435)
                      +.++|||+|||+++|+++|+++|++||.            |..+.+..+++||||+|.+.++|..|+ .||+..|.|  +
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~------------i~~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~   83 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGS------------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSC------------EEEEEECSSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcc------------cceEeeeccccEEEeccCCHHHHHHHHHHhCCCEeCCCce
Confidence            4689999999999999999999999987            677888888999999999999999999 699999987  5


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      +|+|.|+...
T Consensus        84 ~l~v~~ak~~   93 (97)
T d1whya_          84 RLRVDFAKSG   93 (97)
T ss_dssp             BCEEEECCCC
T ss_pred             EEEEEeCCCC
Confidence            8999998653

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=7e-15  Score=113.64  Aligned_cols=74  Identities=26%  Similarity=0.313  Sum_probs=64.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec-CCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          174 ARRVYVGGLPP-LANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN-HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       174 ~~~l~V~nlp~-~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~-~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      +++|||+|||+ .+|+++|+++|+.||.            |..+.+. ..+|||||+|.+.++|.+|+ .|||..|.|+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~------------I~~v~i~~~~kg~afV~f~~~~~A~~ai~~lng~~l~g~~   69 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGD------------VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKP   69 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTC------------EEEEEECCTTSCCEEEEESCHHHHHHHHHHHTTCBCSSSB
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccc------------cceEEEEecccceEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            57899999965 5999999999999998            5555544 34799999999999999999 69999999999


Q ss_pred             EEEcCCCCC
Q 013837          251 VRVRRPTDY  259 (435)
Q Consensus       251 l~v~~~~~~  259 (435)
                      |.|.++...
T Consensus        70 l~v~~s~~~   78 (109)
T d2adca1          70 IRITLSKHQ   78 (109)
T ss_dssp             CEEECCSCC
T ss_pred             EEEEECCCC
Confidence            999997644

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=7.6e-16  Score=113.60  Aligned_cols=77  Identities=17%  Similarity=0.129  Sum_probs=65.0

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAV  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l  251 (435)
                      ...+|||+|||+.+++++|+++|..||.+....      .+.....+.++|||||+|.+.++|.+|+ +||+..|.|++|
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~------~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i   81 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV------CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   81 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTC------EEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEE------EEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEE
Confidence            345799999999999999999999999864421      2333345677899999999999999999 699999999999


Q ss_pred             EEcC
Q 013837          252 RVRR  255 (435)
Q Consensus       252 ~v~~  255 (435)
                      .|.+
T Consensus        82 ~v~l   85 (86)
T d2cqpa1          82 KLVL   85 (86)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9975

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=4.4e-15  Score=113.44  Aligned_cols=76  Identities=18%  Similarity=0.167  Sum_probs=68.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH-h--CCceecC
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA-L--DGIIFEG  248 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~-l--~~~~~~g  248 (435)
                      .++++|||+|||..+|+++|.++|..||.            |..+.+.+.++||||+|.+.++|..|+. +  ++..+.|
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~------------I~~~~~~~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGT------------ICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSC------------EEEEEEETTTTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhccc------------ceEEEEEecceeEEEEeCCHHHHHHHHHHHcCCCcEEee
Confidence            46789999999999999999999999997            6777788899999999999999999993 4  6788999


Q ss_pred             ceEEEcCCCCC
Q 013837          249 VAVRVRRPTDY  259 (435)
Q Consensus       249 ~~l~v~~~~~~  259 (435)
                      ++|+|.|+...
T Consensus        81 ~~l~v~~s~~~   91 (104)
T d1wexa_          81 QQAFFNYSTSK   91 (104)
T ss_dssp             SBCEEEECSSS
T ss_pred             EEEEEEEcCCC
Confidence            99999998654

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.8e-15  Score=117.31  Aligned_cols=77  Identities=14%  Similarity=0.137  Sum_probs=67.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCH-HHHHHHHHHhCCceeCCeEEEEEE
Q 013837          292 EGPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDP-AVTDIACAALNGLKMGDKTLTVRR  370 (435)
Q Consensus       292 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~-~~A~~Al~~l~g~~~~g~~l~V~~  370 (435)
                      .....+||+|||..+|+++|+++|++||.|..|.|+++      +|||||.|.+. ++|..|+..||+..+.++.+.|.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            34456799999999999999999999999999999864      68999999995 789999999999999888888888


Q ss_pred             ccCC
Q 013837          371 ATAS  374 (435)
Q Consensus       371 a~~~  374 (435)
                      +...
T Consensus        83 ~~~~   86 (113)
T d1owxa_          83 EVLE   86 (113)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            7543

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4.7e-15  Score=112.21  Aligned_cols=65  Identities=22%  Similarity=0.338  Sum_probs=58.6

Q ss_pred             CCCCCeEEEcC--CCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCcee
Q 013837          291 AEGPDRVFVGG--LPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKM  361 (435)
Q Consensus       291 ~~~~~~l~V~n--Lp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~  361 (435)
                      ..++.+|+|.|  ||..+|+++|+++|++||.|..|.++.+      +|||||+|.+.++|.+|+..|||..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            35567888855  9999999999999999999999988765      57999999999999999999999987

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=7.3e-15  Score=110.54  Aligned_cols=76  Identities=25%  Similarity=0.385  Sum_probs=63.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEe-------cCCCcEEEEEecCHHHHHHHH-HhC--C
Q 013837          174 ARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYI-------NHEKKFAFVEMRTVEEASNAM-ALD--G  243 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~-------~~~~g~afv~f~~~~~a~~a~-~l~--~  243 (435)
                      .|+|||+|||..+|+++|+++|..||..           +..+.+       +.++|||||+|.+.++|..|+ .|+  +
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~-----------i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~   69 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEG-----------VLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR   69 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTT-----------EEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCc-----------ceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCC
Confidence            3689999999999999999999999963           333333       457899999999999999999 465  4


Q ss_pred             ceecCceEEEcCCCCCC
Q 013837          244 IIFEGVAVRVRRPTDYN  260 (435)
Q Consensus       244 ~~~~g~~l~v~~~~~~~  260 (435)
                      ..+.|++|.|.|+.+..
T Consensus        70 ~~~~g~~i~V~~A~p~~   86 (96)
T d2disa1          70 IQLWGHQIAVDWAEPEI   86 (96)
T ss_dssp             SCBTTBCCEEEESCSSC
T ss_pred             eEECCEEEEEEEcCCCC
Confidence            56789999999987543

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.7e-15  Score=114.23  Aligned_cols=74  Identities=23%  Similarity=0.411  Sum_probs=64.0

Q ss_pred             ccCCeEEEcCCC-CCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCc
Q 013837          172 RHARRVYVGGLP-PLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGV  249 (435)
Q Consensus       172 ~~~~~l~V~nlp-~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~  249 (435)
                      ...++|||+||| ..+++++|+++|.+||.            |..+.+  .+|||||+|.+.++|.+|| .|||..|.|+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~------------i~~~~i--~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~   78 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGK------------IVGCSV--HKGFAFVQYVNERNARAAVAGEDGRMIAGQ   78 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSC------------EEEEEE--ETEEEEEEESSHHHHHHHHHTTTTCEETTE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCC------------EEEEEE--eCCeEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            345689999997 56889999999999997            555555  5899999999999999999 5999999999


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      +|.|.++...
T Consensus        79 ~l~V~~a~~~   88 (98)
T d1wf2a_          79 VLDINLAAEP   88 (98)
T ss_dssp             ECEEEETTSC
T ss_pred             EEEEEECCCC
Confidence            9999997643

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=1.7e-15  Score=111.82  Aligned_cols=70  Identities=23%  Similarity=0.257  Sum_probs=62.1

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      .+|||+|||+.+|+++|+++|++||.            |..+.+. ..|||||+|.+.++|.+|| .|+|..|.|+.|.|
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~------------v~~~~i~-~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v   67 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGD------------VCYADVY-RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   67 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSC------------EEEEEEC-TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcc------------ccccccc-ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEE
Confidence            36999999999999999999999997            5555554 4599999999999999999 69999999999999


Q ss_pred             cCCC
Q 013837          254 RRPT  257 (435)
Q Consensus       254 ~~~~  257 (435)
                      .++.
T Consensus        68 ~~~~   71 (87)
T d3begb1          68 AYIR   71 (87)
T ss_dssp             CBCE
T ss_pred             eEEe
Confidence            8764

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.6e-16  Score=118.09  Aligned_cols=81  Identities=12%  Similarity=0.072  Sum_probs=66.9

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....+|||+|||+.+|+++|.++|..||.+....      .+.....+.++|||||+|.+.++|.+||++|+..|+|+.|
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~------~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i   79 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAV------HVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREA   79 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTE------EECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEE------EEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEE
Confidence            3456899999999999999999999999753310      1122235678999999999999999999999999999999


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|.++..
T Consensus        80 ~V~~~~~   86 (103)
T d2cpya1          80 FVHVVTL   86 (103)
T ss_dssp             EEEEECH
T ss_pred             EEEECCH
Confidence            9987643

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=6.5e-16  Score=118.24  Aligned_cols=82  Identities=18%  Similarity=0.193  Sum_probs=66.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEE
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVR  252 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~  252 (435)
                      ...+|||+|||+++|+++|+++|..+|.+....      .+.....+..+|||||+|.+.++|.+|+++++..|.|+.|.
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v------~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~   87 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGM------TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIE   87 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEE------ECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEE------EEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEE
Confidence            456799999999999999999999998753210      01112234568999999999999999999999999999999


Q ss_pred             EcCCCCCC
Q 013837          253 VRRPTDYN  260 (435)
Q Consensus       253 v~~~~~~~  260 (435)
                      |.++....
T Consensus        88 V~~~~~~~   95 (104)
T d1wg5a_          88 IFKSSRAE   95 (104)
T ss_dssp             EEEECTTT
T ss_pred             EEECCHHH
Confidence            98776543

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=8.9e-16  Score=119.03  Aligned_cols=80  Identities=19%  Similarity=0.186  Sum_probs=67.1

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....+|||+|||+.+|+++|.+||..||.+...      ..+.....+..+|||||+|.+.++|.+||++|+..|+|+.|
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~------~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i   89 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDS------IYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI   89 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTT------CEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCB
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccc------eeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEE
Confidence            456789999999999999999999999876432      11333345677899999999999999999999999999999


Q ss_pred             EEcCCC
Q 013837          252 RVRRPT  257 (435)
Q Consensus       252 ~v~~~~  257 (435)
                      .|..+.
T Consensus        90 ~V~~~~   95 (112)
T d1wela1          90 QVHPIT   95 (112)
T ss_dssp             EEEEEC
T ss_pred             EEEEcC
Confidence            998654

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=2.1e-15  Score=114.04  Aligned_cols=77  Identities=23%  Similarity=0.332  Sum_probs=67.8

Q ss_pred             cccCCeEEEcCCCCC-CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hCCcee
Q 013837          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIF  246 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~~~~~  246 (435)
                      ...+++|||+|||.. +|+++|.++|+.||.            |..+.+..++|||||+|.+.++|..|++   +++..|
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~------------V~~v~~~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~   82 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGK------------IKNYILMRMKSQAFIEMETREDAMAMVDHCLKKALWF   82 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSC------------CSEEEEETTTTEEEEECSSHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccc------------eeEEEEeecCCcEEEEecchHHHHHHHHHHhcCCceE
Confidence            356789999999985 899999999999997            5566777889999999999999999983   889999


Q ss_pred             cCceEEEcCCCCC
Q 013837          247 EGVAVRVRRPTDY  259 (435)
Q Consensus       247 ~g~~l~v~~~~~~  259 (435)
                      .|+.|.|.++..+
T Consensus        83 ~gr~l~V~~s~~~   95 (99)
T d1x4fa1          83 QGRCVKVDLSEKY   95 (99)
T ss_dssp             SSSCCEEEEECSC
T ss_pred             CCEEEEEEEcCCc
Confidence            9999999987654

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=9.2e-15  Score=110.09  Aligned_cols=74  Identities=23%  Similarity=0.266  Sum_probs=64.5

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCce
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~  250 (435)
                      ....+|||+|||+.+++++|+++|..||.            |..+.+. .+|||||+|.+.++|.+|| .||+..|.|+.
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~------------v~~~~i~-~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~   79 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGD------------VCYADVQ-KDGMGMVEYLRKEDMEYALRKLDDTKFRSHE   79 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSC------------EEEEEEE-TTTEEEEEESSHHHHHHHHHHHSSEEEECTT
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcc------------ccccccc-ccceEEEEECCHHHHHHHHHHhCCCEeCCeE
Confidence            35678999999999999999999999997            4445544 5799999999999999999 69999999999


Q ss_pred             EEEcCCCC
Q 013837          251 VRVRRPTD  258 (435)
Q Consensus       251 l~v~~~~~  258 (435)
                      |.|.+...
T Consensus        80 i~v~~~~~   87 (98)
T d1wg4a_          80 GETSYIRV   87 (98)
T ss_dssp             SCEEEEEE
T ss_pred             EEEEEEec
Confidence            99987643

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=9.1e-16  Score=116.92  Aligned_cols=80  Identities=26%  Similarity=0.134  Sum_probs=64.7

Q ss_pred             ccCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceE
Q 013837          172 RHARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAV  251 (435)
Q Consensus       172 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l  251 (435)
                      ....+|||+|||+++|+++|+++|..||.+ .+       .+.....+..+|||||+|.+.++|.+|+++|+..|+|+.|
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~~-~v-------~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I   84 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RV-------HIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYV   84 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EE-------EEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCcc-ee-------eeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEE
Confidence            456789999999999999999999998632 10       0111123456899999999999999999999999999999


Q ss_pred             EEcCCCCC
Q 013837          252 RVRRPTDY  259 (435)
Q Consensus       252 ~v~~~~~~  259 (435)
                      .|.++...
T Consensus        85 ~V~~s~~~   92 (102)
T d1weza_          85 ELFLNSTA   92 (102)
T ss_dssp             EEEEECCC
T ss_pred             EEEEcCCC
Confidence            99986643

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=1.8e-14  Score=108.57  Aligned_cols=79  Identities=18%  Similarity=0.357  Sum_probs=67.9

Q ss_pred             CCCCeEEEcCC--CCCC---------CHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCce
Q 013837          292 EGPDRVFVGGL--PYYF---------TETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLK  360 (435)
Q Consensus       292 ~~~~~l~V~nL--p~~~---------te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~  360 (435)
                      ...++|+|.||  |..+         .++||++.|++||.|..|.+..+    ..+|||||+|.+.++|.+|+..|||.+
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45679999999  5432         23689999999999999988765    357999999999999999999999999


Q ss_pred             eCCeEEEEEEccCC
Q 013837          361 MGDKTLTVRRATAS  374 (435)
Q Consensus       361 ~~g~~l~V~~a~~~  374 (435)
                      |+|+.|.|.|+..+
T Consensus        82 ~~gr~i~v~~~~g~   95 (99)
T d2dita1          82 FGGRQITAQAWDGT   95 (99)
T ss_dssp             ETTEECEEEECCSC
T ss_pred             ECCEEEEEEEeCCc
Confidence            99999999998654

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.51  E-value=9.3e-15  Score=107.95  Aligned_cols=77  Identities=22%  Similarity=0.222  Sum_probs=68.9

Q ss_pred             cccCCeEEEcCCCCC-CCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH---hCCcee
Q 013837          171 TRHARRVYVGGLPPL-ANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA---LDGIIF  246 (435)
Q Consensus       171 ~~~~~~l~V~nlp~~-~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~---l~~~~~  246 (435)
                      ...+++|||+|||.. +|++||.++|++||.            |..+.+..++++|||+|.+.++|..|+.   .++..+
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~------------I~~i~i~~~k~~afV~f~~~~~A~~A~~~l~~~~~~~   72 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGV------------ISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPALV   72 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSC------------EEEEEECSSSSCEEEEESSHHHHHHHHHHHHHSCCEE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCC------------eEEEEeeccceEEEEEEcchhhHHHHHHHHhhCCCcc
Confidence            457889999999986 899999999999997            7788888899999999999999999993   478899


Q ss_pred             cCceEEEcCCCCC
Q 013837          247 EGVAVRVRRPTDY  259 (435)
Q Consensus       247 ~g~~l~v~~~~~~  259 (435)
                      .|++|.|.|++..
T Consensus        73 ~gr~l~V~~s~~~   85 (89)
T d1x4da1          73 FGKPVRVHLSQKY   85 (89)
T ss_dssp             TTEECEEEEECCC
T ss_pred             CCceEEEEECCCc
Confidence            9999999997644

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=1e-14  Score=111.15  Aligned_cols=81  Identities=11%  Similarity=0.205  Sum_probs=69.5

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHHhcCCeeEEEEeecCCCC--CcceEEEEEEcCHHHHHHHHHHhCCc
Q 013837          292 EGPDRVFVGGL--PYYFT--------ETQIKELLESFGTLHGFDLVKDRDTG--NSKGYGFCVYQDPAVTDIACAALNGL  359 (435)
Q Consensus       292 ~~~~~l~V~nL--p~~~t--------e~~l~~~F~~~G~v~~v~i~~~~~tg--~~~G~afV~f~~~~~A~~Al~~l~g~  359 (435)
                      .++++|+|.||  |..+.        .+||++.|++||.|+.|.|+++..+.  ...|+|||+|.+.++|.+|+..|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            35678999999  44432        36899999999999999998876543  35689999999999999999999999


Q ss_pred             eeCCeEEEEEEcc
Q 013837          360 KMGDKTLTVRRAT  372 (435)
Q Consensus       360 ~~~g~~l~V~~a~  372 (435)
                      +|+|+.|.|.|+.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999984

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=7.1e-15  Score=113.15  Aligned_cols=77  Identities=17%  Similarity=0.170  Sum_probs=64.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee--cCc
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF--EGV  249 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~--~g~  249 (435)
                      ...+|||+|||+.+|+++|+++|++||.|..          +.+....++|||||+|.+.++|..|+ .|||..|  .|+
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~----------~~i~~~~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~   75 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLK----------IITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACC   75 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEE----------EEEEEETTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCC
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEE----------EEEEeeCCCCeEEEEECCHHHHHHHHHHHCCCEeccCCc
Confidence            4567999999999999999999999998532          22334467899999999999999999 6999988  478


Q ss_pred             eEEEcCCCCC
Q 013837          250 AVRVRRPTDY  259 (435)
Q Consensus       250 ~l~v~~~~~~  259 (435)
                      .|.|.++...
T Consensus        76 ~l~v~~s~~~   85 (108)
T d2adba1          76 TLRIDFSKLT   85 (108)
T ss_dssp             CCEEEECSSC
T ss_pred             EEEEEecCCc
Confidence            8999887643

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.47  E-value=8.4e-16  Score=109.23  Aligned_cols=70  Identities=20%  Similarity=0.352  Sum_probs=57.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEE
Q 013837          177 VYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVR  252 (435)
Q Consensus       177 l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~  252 (435)
                      |||+|||+++|+++|+++|..||.|..+.      .+.+..++.++|||||+|.+.++|..|+ .|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~------~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTK------AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEE------EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccc------cccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999854310      0111123457899999999999999999 6999999998764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.47  E-value=1.3e-14  Score=107.26  Aligned_cols=69  Identities=19%  Similarity=0.335  Sum_probs=58.2

Q ss_pred             CCeEEEcCCCCCCCHHHH---HHHHHHHHHhhcCCCCCCCCceEEEEe------cC---CCcEEEEEecCHHHHHHHH-H
Q 013837          174 ARRVYVGGLPPLANEQAI---ATFFSQVMTAIGGNSAGPGDAVVNVYI------NH---EKKFAFVEMRTVEEASNAM-A  240 (435)
Q Consensus       174 ~~~l~V~nlp~~~t~~~l---~~~f~~~G~i~~~~~~~~~~~v~~~~~------~~---~~g~afv~f~~~~~a~~a~-~  240 (435)
                      .++|||+|||+.+++++|   .++|.+||.|..            +.+      +.   .+|||||+|.+.++|..|+ .
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~------------v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~   75 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHK------------VVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC   75 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEE------------EEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHH
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceE------------EEEeeccCcCCCCCcceEEEEecccchhHHHHHHH
Confidence            457999999999999999   678999998543            332      12   2489999999999999999 6


Q ss_pred             hCCceecCceEEEc
Q 013837          241 LDGIIFEGVAVRVR  254 (435)
Q Consensus       241 l~~~~~~g~~l~v~  254 (435)
                      |||..|.|++|+|.
T Consensus        76 lng~~~~gr~lkvS   89 (89)
T d2cpia1          76 VNNVVVDGRTLKAS   89 (89)
T ss_dssp             HTTEEETTEEEEEE
T ss_pred             hCCCEECCEEEEEC
Confidence            99999999999873

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.46  E-value=2.8e-14  Score=108.43  Aligned_cols=76  Identities=9%  Similarity=0.008  Sum_probs=65.9

Q ss_pred             cCCeEEEcCCCCCC-C----HHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCcee
Q 013837          173 HARRVYVGGLPPLA-N----EQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIF  246 (435)
Q Consensus       173 ~~~~l~V~nlp~~~-t----~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~  246 (435)
                      ...+|||+||+..+ +    +++|.++|+.||.            |+.+.+.++++||||+|.+.++|.+|+ .|||..|
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~------------i~~~~~~k~~~~afV~f~~~~~A~~Ai~~lng~~~   71 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDK------------DTTFQYFKSFKRVRINFSNPLSAADARLRLHKTEF   71 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCS------------SCEEEEETTTTEEEEECSSTTHHHHHHHTSTTSEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhccccc------------ceEEEEecCCCEEEEEECCHHHHHHHHHHhccccc
Confidence            46789999999886 3    3668999999987            566777789999999999999999999 6999999


Q ss_pred             cCceEEEcCCCCCC
Q 013837          247 EGVAVRVRRPTDYN  260 (435)
Q Consensus       247 ~g~~l~v~~~~~~~  260 (435)
                      .|++|+|.|+....
T Consensus        72 ~g~~l~v~~a~~~~   85 (104)
T d1weya_          72 LGKEMKLYFAQTLH   85 (104)
T ss_dssp             TTEECEEECCCCSS
T ss_pred             CCCEeEEeecccCC
Confidence            99999999986543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=5.5e-14  Score=101.21  Aligned_cols=72  Identities=15%  Similarity=0.196  Sum_probs=61.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCe-EEEEEEccC
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDK-TLTVRRATA  373 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~-~l~V~~a~~  373 (435)
                      +.|+|.|+|+.++++.| .+|++||.|.++.+..      .+|||||+|.+.++|.+||+ +||..|+|+ .|.|..+..
T Consensus         5 ~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           5 TWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECCC
T ss_pred             cEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCCC
Confidence            57999999999987655 5799999999988754      37899999999999999996 999999997 467988854


Q ss_pred             C
Q 013837          374 S  374 (435)
Q Consensus       374 ~  374 (435)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            3

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=1.8e-13  Score=116.04  Aligned_cols=81  Identities=26%  Similarity=0.514  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEccC
Q 013837          294 PDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRATA  373 (435)
Q Consensus       294 ~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~~  373 (435)
                      .++|||+|||+.+|+++|+++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..+.++.+.+.....
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            3689999999999999999999999999999999999999999999999999999999998 577888899888887755


Q ss_pred             CC
Q 013837          374 SS  375 (435)
Q Consensus       374 ~~  375 (435)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            43

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=3.7e-13  Score=96.79  Aligned_cols=73  Identities=19%  Similarity=0.285  Sum_probs=62.9

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCce-E
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVA-V  251 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~-l  251 (435)
                      +.+.|+|.|+|+.++++.| .+|++||.            |.++.++.+++||||+|.+.++|.+||++||..|+|+. |
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~------------I~~~~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~v   69 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGN------------ILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMI   69 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSC------------EEEEEECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhh------------hheEEecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEE
Confidence            3567999999999986555 68999997            77888899999999999999999999999999999985 5


Q ss_pred             EEcCCCC
Q 013837          252 RVRRPTD  258 (435)
Q Consensus       252 ~v~~~~~  258 (435)
                      .|..+.+
T Consensus        70 gV~~~~~   76 (81)
T d1wwha1          70 GVKPCID   76 (81)
T ss_dssp             EEEECCC
T ss_pred             EEEeCCC
Confidence            6876543

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.35  E-value=1.1e-12  Score=98.85  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=57.2

Q ss_pred             ccCCeEEEcC--CCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          172 RHARRVYVGG--LPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       172 ~~~~~l~V~n--lp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      .+.++|+|.|  ||..+|+++|+++|.+||.            |..+.+..+++||||+|.+.++|..|+ .|||..+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~------------i~~i~~~~~k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGL------------VDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSC------------EEEEECCTTCSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCc------------ccEEeeccCccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            4567899955  9999999999999999997            777888889999999999999999999 69998773

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=2.1e-12  Score=99.72  Aligned_cols=72  Identities=11%  Similarity=0.040  Sum_probs=61.2

Q ss_pred             cCCeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCH-HHHHHHH-HhCCceecCce
Q 013837          173 HARRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTV-EEASNAM-ALDGIIFEGVA  250 (435)
Q Consensus       173 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~-~~a~~a~-~l~~~~~~g~~  250 (435)
                      ....+||+|||+.+|+++|+++|.+||.            |..+.+..++|||||.|.+. ++|..|+ .+++..+.++.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~------------V~~v~i~~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~   77 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGE------------IKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQLRN   77 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCC------------EEEEECCTTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCC------------hheEEEecCCceEEEEecCcHHHHHHHHHHhcCCceecCc
Confidence            3456799999999999999999999997            77888888999999999985 7788888 69998888776


Q ss_pred             EEEcCC
Q 013837          251 VRVRRP  256 (435)
Q Consensus       251 l~v~~~  256 (435)
                      +.|.+.
T Consensus        78 ~~v~~~   83 (113)
T d1owxa_          78 KEVTWE   83 (113)
T ss_dssp             SSEEEE
T ss_pred             eEEEEe
Confidence            666543

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=3.2e-12  Score=96.77  Aligned_cols=75  Identities=17%  Similarity=0.129  Sum_probs=61.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH-HhCCceecCceEEE
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRV  253 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v  253 (435)
                      ..++|.+++..++|++|.++|++||.|..+.       |.....+.++|||||+|.+.++|.+|+ .|||..|+|++|.|
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~-------I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v  100 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN-------VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA  100 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEE-------ECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEE-------eecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEE
Confidence            3588899999999999999999999854421       111123567899999999999999999 69999999999999


Q ss_pred             cCC
Q 013837          254 RRP  256 (435)
Q Consensus       254 ~~~  256 (435)
                      .+.
T Consensus       101 ~~s  103 (104)
T d1jmta_         101 ELS  103 (104)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            863

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=4.1e-11  Score=89.79  Aligned_cols=78  Identities=23%  Similarity=0.255  Sum_probs=62.0

Q ss_pred             cccCCeEEEcCC--CCCC---------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHH
Q 013837          171 TRHARRVYVGGL--PPLA---------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAM  239 (435)
Q Consensus       171 ~~~~~~l~V~nl--p~~~---------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~  239 (435)
                      ...+++|+|.||  |.++         .+++|++.|.+||.|.          .+.+..+..+|||||+|.+.++|.+|+
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~----------~v~~~~~~~~G~~fV~f~~~e~A~~A~   74 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIR----------KLLLFDRHPDGVASVSFRDPEEADYCI   74 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCS----------EEEEETTCTTCEEEEECSCHHHHHHHH
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEE----------EEeccCCCCccEEEEEECCHHHHHHHH
Confidence            457889999999  5432         1367888888888753          233445567899999999999999999


Q ss_pred             -HhCCceecCceEEEcCCCC
Q 013837          240 -ALDGIIFEGVAVRVRRPTD  258 (435)
Q Consensus       240 -~l~~~~~~g~~l~v~~~~~  258 (435)
                       .|||..|+|++|.|.+...
T Consensus        75 ~~lng~~~~gr~i~v~~~~g   94 (99)
T d2dita1          75 QTLDGRWFGGRQITAQAWDG   94 (99)
T ss_dssp             HHSTTCEETTEECEEEECCS
T ss_pred             HHhCCcEECCEEEEEEEeCC
Confidence             6999999999999997653

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=7.7e-10  Score=83.56  Aligned_cols=73  Identities=18%  Similarity=0.128  Sum_probs=58.4

Q ss_pred             cCCeEEEcCC--CCCC--------CHHHHHHHHHHHHHhhcCCCCCCCCceEEEEec--------CCCcEEEEEecCHHH
Q 013837          173 HARRVYVGGL--PPLA--------NEQAIATFFSQVMTAIGGNSAGPGDAVVNVYIN--------HEKKFAFVEMRTVEE  234 (435)
Q Consensus       173 ~~~~l~V~nl--p~~~--------t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~--------~~~g~afv~f~~~~~  234 (435)
                      +++.|+|.||  |..+        ..++|++.|.+||.|            ..+.+.        ...|++||+|.+.++
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v------------~~v~I~~~~~~~~~~~~g~vfV~f~~~e~   70 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLV------------KSIEIPRPVDGVEVPGCGKIFVEFTSVFD   70 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCE------------EEEECCCCTTSSSCTTCCEEEEEESCHHH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCce------------EEEEEeecCCCCccCCceEEEEEECCHHH
Confidence            4678999999  4443        236788999999984            444432        235899999999999


Q ss_pred             HHHHH-HhCCceecCceEEEcCCC
Q 013837          235 ASNAM-ALDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       235 a~~a~-~l~~~~~~g~~l~v~~~~  257 (435)
                      |.+|+ .|+|..++|+.|.|.+..
T Consensus        71 A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          71 CQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             HHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             HHHHHHHHCCCEECCeEEEEEEcC
Confidence            99999 699999999999998754

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=6.8e-06  Score=54.27  Aligned_cols=61  Identities=20%  Similarity=0.218  Sum_probs=53.1

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       309 ~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      +.|.+.|.++|.|..+.|....+ |..  .|-|...+.++|..|+..||-.+|+++.|.|.|++
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-CcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45667899999999999877643 443  58999999999999999999999999999999985

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.85  E-value=3.4e-05  Score=53.66  Aligned_cols=55  Identities=15%  Similarity=0.294  Sum_probs=48.9

Q ss_pred             HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHhCCceeCCeEEEEEEcc
Q 013837          309 TQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAALNGLKMGDKTLTVRRAT  372 (435)
Q Consensus       309 ~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l~g~~~~g~~l~V~~a~  372 (435)
                      .+|.+.|..||.|.-|+++.+        ..+|.|.+-+.|.+|++ |+|.+++|+.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCC
Confidence            468888999999988888876        57899999999999999 89999999999998653

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.84  E-value=4.6e-05  Score=54.06  Aligned_cols=79  Identities=15%  Similarity=0.183  Sum_probs=63.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCC--cceEEEEEEcCHHHHHHHHHHhCCceeCC-----eEEE
Q 013837          295 DRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGN--SKGYGFCVYQDPAVTDIACAALNGLKMGD-----KTLT  367 (435)
Q Consensus       295 ~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~--~~G~afV~f~~~~~A~~Al~~l~g~~~~g-----~~l~  367 (435)
                      ++|.|+.||+.+||+++.+.+...|.+........+.+.+  .-.-|||.|.+.++.....+.++|+.|-+     ..-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            5799999999999999999999999988877777654322  12459999999999999999999998832     2457


Q ss_pred             EEEccC
Q 013837          368 VRRATA  373 (435)
Q Consensus       368 V~~a~~  373 (435)
                      |+||--
T Consensus        82 VE~AP~   87 (91)
T d1uw4a_          82 VEFAPF   87 (91)
T ss_dssp             EEECSS
T ss_pred             EEEcCc
Confidence            888743

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.98  E-value=0.00056  Score=47.42  Aligned_cols=54  Identities=24%  Similarity=0.332  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHHhCCceecCceEEEcCC
Q 013837          189 QAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMALDGIIFEGVAVRVRRP  256 (435)
Q Consensus       189 ~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~l~~~~~~g~~l~v~~~  256 (435)
                      .+|.+.|..||+|            +.+++.  .+..+|+|.+-+.|.+|+.++|.++.|+.|+|...
T Consensus        39 ~~Llq~l~~~GeV------------iLvRFv--~d~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          39 TELMQTLGSYGTI------------VLVRIN--QGQMLVTFADSHSALSVLDVDGMKVKGRAVKISGP   92 (95)
T ss_dssp             HHHHHHHHHHSCC------------SEEEEE--TTEEEEECSCSHHHHHHHHGGGSEETTEEEEEECC
T ss_pred             HHHHHHHhhCCeE------------EEEEEe--CCeEEEEECCcHHHHHHhccCCeEEcceEEEEecC
Confidence            4566777777763            333332  35789999999999999999999999999999754

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.33  E-value=0.0086  Score=42.10  Aligned_cols=56  Identities=20%  Similarity=0.401  Sum_probs=46.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEEcCHHHHHHHHHHh
Q 013837          293 GPDRVFVGGLPYYFTETQIKELLESFGTLHGFDLVKDRDTGNSKGYGFCVYQDPAVTDIACAAL  356 (435)
Q Consensus       293 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~v~i~~~~~tg~~~G~afV~f~~~~~A~~Al~~l  356 (435)
                      ....||.-..|..+...||.++|++||.|. |..+-+.       -|||...+.++|..++..+
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHh
Confidence            345689999999999999999999999974 5555442       6999999999999888754

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.10  E-value=0.0031  Score=44.37  Aligned_cols=64  Identities=16%  Similarity=0.290  Sum_probs=47.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecC------CCcEEEEEecCHHHHHHHH-HhCCceec
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINH------EKKFAFVEMRTVEEASNAM-ALDGIIFE  247 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~------~~g~afv~f~~~~~a~~a~-~l~~~~~~  247 (435)
                      .+|.|+.||+.+||+++.+.+...|.+-          .....-+.      .-.-|||.|.+.++..... .++|+.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d----------~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHD----------YFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEE----------EEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceE----------EEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4799999999999999999887665421          11111221      1258999999999999988 59998885


Q ss_pred             C
Q 013837          248 G  248 (435)
Q Consensus       248 g  248 (435)
                      +
T Consensus        72 D   72 (91)
T d1uw4a_          72 D   72 (91)
T ss_dssp             C
T ss_pred             c
Confidence            4

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.75  E-value=0.011  Score=38.59  Aligned_cols=57  Identities=21%  Similarity=0.210  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCceEEEEec---CCCcEEEEEecCHHHHHHHH-HhCCceecCceEEEcCCC
Q 013837          189 QAIATFFSQVMTAIGGNSAGPGDAVVNVYIN---HEKKFAFVEMRTVEEASNAM-ALDGIIFEGVAVRVRRPT  257 (435)
Q Consensus       189 ~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~---~~~g~afv~f~~~~~a~~a~-~l~~~~~~g~~l~v~~~~  257 (435)
                      +.|.+.|.++|.            |..+.+-   ...-.|-|...+.++|..|+ .|+...|+++.|.|.+++
T Consensus        11 q~L~~~f~~h~~------------V~sv~l~~~~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGK------------VKSVELSPHTDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSC------------EEEEEECSCCSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhhee------------EEEEEEEeccCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            345567778876            4555442   23458999999999999999 699999999999998764

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.56  E-value=0.32  Score=33.82  Aligned_cols=52  Identities=17%  Similarity=0.187  Sum_probs=42.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHHHHHHhhcCCCCCCCCceEEEEecCCCcEEEEEecCHHHHHHHHH
Q 013837          175 RRVYVGGLPPLANEQAIATFFSQVMTAIGGNSAGPGDAVVNVYINHEKKFAFVEMRTVEEASNAMA  240 (435)
Q Consensus       175 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~v~~~~~~~~~g~afv~f~~~~~a~~a~~  240 (435)
                      .-||.-.+|......||.++|.+||.|.          |.-+    +-.-|||...+.++|..++.
T Consensus        16 dHVf~~tFP~~Wk~~dI~~lFSpfG~V~----------VswI----ddTSa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          16 DHVLHVTFPKEWKTSDLYQLFSAFGNIQ----------ISWI----DDTSAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CSEEEEECCTTCCHHHHHHHHTTTCSCC----------CEEE----ETTEEEEECSCHHHHHHHHH
T ss_pred             ceeEEEeCCcccchhHHHHHhcCCCceE----------EEEe----cCceEEEEecCHHHHHHHHH
Confidence            4599999999999999999999998751          2222    33489999999999999884